@article {pmid33471121,
year = {2021},
author = {Shah, N and Molloy, EK and Pop, M and Warnow, T},
title = {TIPP2: metagenomic taxonomic profiling using phylogenetic markers.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btab023},
pmid = {33471121},
issn = {1367-4811},
abstract = {MOTIVATION: Metagenomics has revolutionized microbiome research by enabling researchers to characterize the composition of complex microbial communities. Taxonomic profiling is one of the critical steps in metagenomic analyses. Marker genes, which are single-copy and universally found across Bacteria and Archaea, can provide accurate estimates of taxon abundances in the sample.<br><br>RESULTS: We present TIPP2, a marker gene-based abundance profiling method, that combines phylogenetic placement with statistical techniques to control classification precision and recall. TIPP2 includes an updated set of reference packages and several algorithmic improvements over the original TIPP method. We find that TIPP2 provides comparable or better estimates of abundance than other profiling methods (including Bracken, mOTUsv2, and MetaPhlAn2), and strictly dominates other methods when there are under-represented (novel) genomes present in the dataset.<br><br>The code for our method is freely available in open source form at https://github.com/smirarab/sepp/blob/tipp2/README.TIPP.mdThe code and procedure to create new reference packages for TIPP2 are available at https://github.com/shahnidhi/TIPP_reference_package.<br><br>SUPPLEMENTARY INFORMATION: Not available online.},
}
@article {pmid33471066,
year = {2021},
author = {Petrillo, UF and Palini, F and Cattaneo, G and Giancarlo, R},
title = {Alignment-free Genomic Analysis via a Big Data Spark Platform.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btab014},
pmid = {33471066},
issn = {1367-4811},
abstract = {MOTIVATION: Alignment-free distance and similarity functions (AF functions, for short) are a well established alternative to pairwise and multiple sequence alignments for many genomic, metagenomic and epigenomic tasks. Due to data-intensive applications, the computation of AF functions is a Big Data problem, with the recent literature indicating that the development of fast and scalable algorithms computing AF functions is a high-priority task. Somewhat surprisingly, despite the increasing popularity of Big Data technologies in computational biology, the development of a Big Data platform for those tasks has not been pursued, possibly due to its complexity.<br><br>RESULTS: We fill this important gap by introducing FADE, the first extensible, efficient and scalable Spark platform for alignment-free genomic analysis. It supports natively eighteen of the best performing AF functions coming out of a recent hallmark benchmarking study. FADE development and potential impact comprises novel aspects of interest. Namely, (a) a considerable effort of distributed algorithms, the most tangible result being a much faster execution time of reference methods like MASH and FSWM; (b) a software design that makes FADE user-friendly and easily extendable by Spark non-specialists; (c) its ability to support data- and compute-intensive tasks. About this, we provide a novel and much needed analysis of how informative and robust AF functions are, in terms of the statistical significance of their output. Our findings naturally extend the ones of the highly regarded benchmarking study, since the functions that can really be used are reduced to a handful of the eighteen included in FADE.<br><br>AVAILABILITY: The software and the datasets are available at https://github.com/fpalini/fade.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid33471063,
year = {2021},
author = {Pons, JC and Paez-Espino, D and Riera, G and Ivanova, N and Kyrpides, NC and Llabrés, M},
title = {VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btab026},
pmid = {33471063},
issn = {1367-4811},
abstract = {MOTIVATION: Two key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been explored for determining viral taxonomy and host targets.<br><br>RESULTS: In this work we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified.<br><br>AVAILABILITY: The implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools.<br><br>SUPPLEMENTARY INFORMATION: http://bioinfo.uib.es/~recerca/VPF-Class/.},
}
@article {pmid33470507,
year = {2021},
author = {Castelli, M and Lanzoni, O and Nardi, T and Lometto, S and Modeo, L and Potekhin, A and Sassera, D and Petroni, G},
title = {&quot;Candidatus Sarmatiella mevalonica&quot; endosymbiont of the ciliate Paramecium provides insights on evolutionary plasticity among Rickettsiales.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15396},
pmid = {33470507},
issn = {1462-2920},
abstract = {Members of the bacterial order Rickettsiales are obligatorily associated with a wide range of eukaryotic hosts. Their evolutionary trajectories, in particular concerning the origin of shared or differential traits among distant sub-lineages, are still poorly understood. Here we characterised a novel Rickettsiales bacterium associated with the ciliate Paramecium tredecaurelia, and phylogenetically related to the Rickettsia genus. Its genome encodes significant lineage-specific features, chiefly the mevalonate pathway gene repertoire, involved in isoprenoid precursor biosynthesis. Not only this pathway has never been described in Rickettsiales, it also is very rare among bacteria, though typical in eukaryotes, thus likely representing a horizontally-acquired trait. The presence of these genes could enable an efficient exploitation of host-derived intermediates for isoprenoid synthesis. Moreover, we hypothesise the reversed reactions could have replaced canonical pathways for producing acetyl-CoA, essential for phospholipid biosynthesis. Additionally, we detected phylogenetically unrelated mevalonate pathway genes in metagenome-derived Rickettsiales sequences, likely indicating evolutionary convergent effects of independent horizontal gene transfer events. Accordingly, convergence, involving both gene acquisitions and losses, is highlighted as a relevant evolutionary phenomenon in Rickettsiales, possibly favoured by plasticity and comparable lifestyles, representing a potentially hidden origin of other more nuanced similarities among sub-lineages. This article is protected by copyright. All rights reserved.},
}
@article {pmid33469805,
year = {2021},
author = {Lyu, Z},
title = {Back to the Source: Molecular Identification of Methanogenic Archaea as Markers of Colonic Methane Production.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {33469805},
issn = {1573-2568},
}
@article {pmid33469669,
year = {2021},
author = {Zhang, K and He, C and Xu, Y and Zhang, C and Li, C and Jing, X and Wang, M and Yang, Y and Suo, L and Kalds, P and Song, J and Wang, X and Brugger, D and Wu, Y and Chen, Y},
title = {Taxonomic and functional adaption of the gastrointestinal microbiome of goats kept at high altitude (4800 m) under intensive or extensive rearing conditions.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiab009},
pmid = {33469669},
issn = {1574-6941},
abstract = {The gut microbiota composition is influenced by the diet as well as the environment in both wild and domestic animals. We studied the effects of two feeding systems on the rumen and hindgut microbiome of semi-feral Tibetan goats kept at high altitude (∼4800 m) using 16S rRNA gene and metagenomic sequencing. Intensive drylot feeding resulted in significantly higher zootechnical performance, narrower ruminal acetate: propionate ratios and a drop in the average rumen pH at slaughter to ∼5.04. Hindgut microbial adaption appeared to be more diverse in the drylot group suggesting a higher influx of undegraded complex non-starch polysaccharides from the rumen. Despite their higher fiber levels in the diet, grazing goats exhibited lower counts of Methanobrevibacter and genes associated with the hydrogenotrophic methanogenesis pathway, presumably reflecting the scarce dietary conditions (low energy density) when rearing goats on pasture from extreme alpine environments. These conditions appeared to promote a relevant abundance of bacitracin genes. In parallel, we recognized a significant increase in the abundance of antibiotic resistance genes in the digestive tracts of drylot animals. In summary, this study provides a deeper insight into the metataxonomic and functional adaption of the gastrointestinal microbiome of goats subject to intensive drylot and extensive pasture rearing conditions at high altitude.},
}
@article {pmid33469166,
year = {2021},
author = {Robbins, SJ and Song, W and Engelberts, JP and Glasl, B and Slaby, BM and Boyd, J and Marangon, E and Botté, ES and Laffy, P and Thomas, T and Webster, NS},
title = {A genomic view of the microbiome of coral reef demosponges.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {33469166},
issn = {1751-7370},
abstract = {Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.},
}
@article {pmid33468706,
year = {2021},
author = {Jing, G and Liu, L and Wang, Z and Zhang, Y and Qian, L and Gao, C and Zhang, M and Li, M and Zhang, Z and Liu, X and Xu, J and Su, X},
title = {Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33468706},
issn = {2379-5077},
abstract = {Metagenomic data sets from diverse environments have been growing rapidly. To ensure accessibility and reusability, tools that quickly and informatively correlate new microbiomes with existing ones are in demand. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes in the global metagenome data space based on the taxonomic or functional similarity of a whole microbiome to those in the database. MSE 2 consists of (i) a well-organized and regularly updated microbiome database that currently contains over 250,000 metagenomic shotgun and 16S rRNA gene amplicon samples associated with unified metadata collected from 798 studies, (ii) an enhanced search engine that enables real-time and fast (<0.5 s per query) searches against the entire database for best-matched microbiomes using overall taxonomic or functional profiles, and (iii) a Web-based graphical user interface for user-friendly searching, data browsing, and tutoring. MSE 2 is freely accessible via http://mse.ac.cn For standalone searches of customized microbiome databases, the kernel of the MSE 2 search engine is provided at GitHub (https://github.com/qibebt-bioinfo/meta-storms).IMPORTANCE A search-based strategy is useful for large-scale mining of microbiome data sets, such as a bird's-eye view of the microbiome data space and disease diagnosis via microbiome big data. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes against the existing microbiome data sets on the basis of their similarity in taxonomic structure or functional profile. Key improvements include database extension, data compatibility, a search engine kernel, and a user interface. The new ability to search the microbiome space via functional similarity greatly expands the scope of search-based mining of the microbiome big data.},
}
@article {pmid33468689,
year = {2021},
author = {Simsek, C and Corman, VM and Everling, HU and Lukashev, AN and Rasche, A and Maganga, GD and Binger, T and Jansen, D and Beller, L and Deboutte, W and Gloza-Rausch, F and Seebens-Hoyer, A and Yordanov, S and Sylverken, A and Oppong, S and Sarkodie, YA and Vallo, P and Leroy, EM and Bourgarel, M and Yinda, KC and Van Ranst, M and Drosten, C and Drexler, JF and Matthijnssens, J},
title = {At Least Seven Distinct Rotavirus Genotype Constellations in Bats with Evidence of Reassortment and Zoonotic Transmissions.},
journal = {mBio},
volume = {12},
number = {1},
pages = {},
pmid = {33468689},
issn = {2150-7511},
abstract = {Bats host many viruses pathogenic to humans, and increasing evidence suggests that rotavirus A (RVA) also belongs to this list. Rotaviruses cause diarrheal disease in many mammals and birds, and their segmented genomes allow them to reassort and increase their genetic diversity. Eighteen out of 2,142 bat fecal samples (0.8%) collected from Europe, Central America, and Africa were PCR-positive for RVA, and 11 of those were fully characterized using viral metagenomics. Upon contrasting their genomes with publicly available data, at least 7 distinct bat RVA genotype constellations (GCs) were identified, which included evidence of reassortments and 6 novel genotypes. Some of these constellations are spread across the world, whereas others appear to be geographically restricted. Our analyses also suggest that several unusual human and equine RVA strains might be of bat RVA origin, based on their phylogenetic clustering, despite various levels of nucleotide sequence identities between them. Although SA11 is one of the most widely used reference strains for RVA research and forms the backbone of a reverse genetics system, its origin remained enigmatic. Remarkably, the majority of the genotypes of SA11-like strains were shared with Gabonese bat RVAs, suggesting a potential common origin. Overall, our findings suggest an underexplored genetic diversity of RVAs in bats, which is likely only the tip of the iceberg. Increasing contact between humans and bat wildlife will further increase the zoonosis risk, which warrants closer attention to these viruses.IMPORTANCE The increased research on bat coronaviruses after severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) allowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general, and bats in particular, for global preparedness against emerging viral pathogens. The current effort to characterize bat rotavirus strains from 3 continents sheds light on the vast genetic diversity of rotaviruses and also hints at a bat origin for several atypical rotaviruses in humans and animals, implying that zoonoses of bat rotaviruses might occur more frequently than currently realized.},
}
@article {pmid33468686,
year = {2021},
author = {Crits-Christoph, A and Kantor, RS and Olm, MR and Whitney, ON and Al-Shayeb, B and Lou, YC and Flamholz, A and Kennedy, LC and Greenwald, H and Hinkle, A and Hetzel, J and Spitzer, S and Koble, J and Tan, A and Hyde, F and Schroth, G and Kuersten, S and Banfield, JF and Nelson, KL},
title = {Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants.},
journal = {mBio},
volume = {12},
number = {1},
pages = {},
pmid = {33468686},
issn = {2150-7511},
abstract = {Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.},
}
@article {pmid33468146,
year = {2021},
author = {Oluyomi, AO and Panthagani, K and Sotelo, J and Gu, X and Armstrong, G and Luo, DN and Hoffman, KL and Rohlman, D and Tidwell, L and Hamilton, WJ and Symanski, E and Anderson, K and Petrosino, JF and Walker, CL and Bondy, M},
title = {Houston hurricane Harvey health (Houston-3H) study: assessment of allergic symptoms and stress after hurricane Harvey flooding.},
journal = {Environmental health : a global access science source},
volume = {20},
number = {1},
pages = {9},
pmid = {33468146},
issn = {1476-069X},
support = {R21ES029616/ES/NIEHS NIH HHS/United States ; R21ES029493)/ES/NIEHS NIH HHS/United States ; R21ES029460/ES/NIEHS NIH HHS/United States ; P30ES030285/ES/NIEHS NIH HHS/United States ; },
abstract = {BACKGROUND: In August 2017, Hurricane Harvey caused unprecedented flooding across the greater Houston area. Given the potential for widespread flood-related exposures, including mold and sewage, and the emotional and mental toll caused by the flooding, we sought to evaluate the short- and long-term impact of flood-related exposures on the health of Houstonians. Our objectives were to assess the association of flood-related exposures with allergic symptoms and stress among Houston-area residents at two time points: within approximately 30 days (T1) and 12 months (T2) after Hurricane Harvey's landfall.<br><br>METHODS: The Houston Hurricane Harvey Health (Houston-3H) Study enrolled a total of 347 unique participants from four sites across Harris County at two times: within approximately 1-month of Harvey (T1, n = 206) and approximately 12-months after Harvey (T2, n = 266), including 125 individuals who participated at both time points. Using a self-administered questionnaire, participants reported details on demographics, flood-related exposures, and health outcomes, including allergic symptoms and stress.<br><br>RESULTS: The majority of participants reported hurricane-related flooding in their homes at T1 (79.1%) and T2 (87.2%) and experienced at least one allergic symptom after the hurricane (79.4% at T1 and 68.4% at T2). In general, flood-exposed individuals were at increased risk of upper respiratory tract allergic symptoms, reported at both the T1 and T2 time points, with exposures to dirty water and mold associated with increased risk of multiple allergic symptoms. The mean stress score of study participants at T1 was 8.0 ± 2.1 and at T2, 5.1 ± 3.2, on a 0-10 scale. Participants who experienced specific flood-related exposures reported higher stress scores when compared with their counterparts, especially 1 year after Harvey. Also, a supplementary paired-samples analysis showed that reports of wheezing, shortness of breath, and skin rash did not change between T1 and T2, though other conditions were less commonly reported at T2.<br><br>CONCLUSION: These initial Houston-3H findings demonstrate that flooding experiences that occurred as a consequence of Hurricane Harvey had lasting impacts on the health of Houstonians up to 1 year after the hurricane.},
}
@article {pmid33468056,
year = {2021},
author = {Zaidi, SSA and Kayani, MUR and Zhang, X and Ouyang, Y and Shamsi, IH},
title = {Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {60},
pmid = {33468056},
issn = {1471-2164},
support = {2012GB316504//National Basic Research Program of China (973 Program)/ ; 31750110462, 31961143008//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Efficient regulation of bacterial genes in response to the environmental stimulus results in unique gene clusters known as operons. Lack of complete operonic reference and functional information makes the prediction of metagenomic operons a challenging task; thus, opening new perspectives on the interpretation of the host-microbe interactions.<br><br>RESULTS: In this work, we identified whole-genome and metagenomic operons via MetaRon (Metagenome and whole-genome opeRon prediction pipeline). MetaRon identifies operons without any experimental or functional information. MetaRon was implemented on datasets with different levels of complexity and information. Starting from its application on whole-genome to simulated mixture of three whole-genomes (E. coli MG1655, Mycobacterium tuberculosis H37Rv and Bacillus subtilis str. 16), E. coli c20 draft genome extracted from chicken gut and finally on 145 whole-metagenome data samples from human gut. MetaRon consistently achieved high operon prediction sensitivity, specificity and accuracy across E. coli whole-genome (97.8, 94.1 and 92.4%), simulated genome (93.7, 75.5 and 88.1%) and E. coli c20 (87, 91 and 88%,), respectively. Finally, we identified 1,232,407 unique operons from 145 paired-end human gut metagenome samples. We also report strong association of type 2 diabetes with Maltose phosphorylase (K00691), 3-deoxy-D-glycero-D-galacto-nononate 9-phosphate synthase (K21279) and an uncharacterized protein (K07101).<br><br>CONCLUSION: With MetaRon, we were able to remove two notable limitations of existing whole-genome operon prediction methods: (1) generalizability (ability to predict operons in unrelated bacterial genomes), and (2) whole-genome and metagenomic data management. We also demonstrate the use of operons as a subset to represent the trends of secondary metabolites in whole-metagenome data and the role of secondary metabolites in the occurrence of disease condition. Using operonic data from metagenome to study secondary metabolic trends will significantly reduce the data volume to more precise data. Furthermore, the identification of metabolic pathways associated with the occurrence of type 2 diabetes (T2D) also presents another dimension of analyzing the human gut metagenome. Presumably, this study is the first organized effort to predict metagenomic operons and perform a detailed analysis in association with a disease, in this case type 2 diabetes. The application of MetaRon to metagenomic data at diverse scale will be beneficial to understand the gene regulation and therapeutic metagenomics.},
}
@article {pmid33467169,
year = {2021},
author = {Piombo, E and Abdelfattah, A and Droby, S and Wisniewski, M and Spadaro, D and Schena, L},
title = {Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/microorganisms9010188},
pmid = {33467169},
issn = {2076-2607},
support = {CLEANFRUIT - Standardization of innovative pest control strategies to produce zero residue fruit for baby food and other fruit produce//European Institute of Innovation and Technology - EITFood/ ; A gnotobiotic-based approach to unravel the role of the plant microbiome and develop synthetic communities increasing plant growth and stress tolerance - NATURE//Italian Ministry for Education, University and Research/ ; SMART APPLE - Innovative and SMART technologies for sustainable APPLE production//Fondazione Cassa di Risparmio di Cuneo/ ; },
abstract = {Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegetables, with a corresponding increase in economic losses caused by the introduction of transboundary plant pathogens. Current diagnostic techniques provide a useful and precise tool to enact surveillance protocols regarding specific organisms, but this approach is strictly targeted, while metabarcoding and shotgun metagenomics could be used to simultaneously detect all known pathogens and potentially new ones. This review aims to present the current status of high-throughput sequencing (HTS) diagnostics of fungal and bacterial plant pathogens, discuss the challenges that need to be addressed, and provide direction for the development of methods for the detection of a restricted number of related taxa (specific surveillance) or all of the microorganisms present in a sample (general surveillance). HTS techniques, particularly metabarcoding, could be useful for the surveillance of soilborne, seedborne and airborne pathogens, as well as for identifying new pathogens and determining the origin of outbreaks. Metabarcoding and shotgun metagenomics still suffer from low precision, but this issue can be limited by carefully choosing primers and bioinformatic algorithms. Advances in bioinformatics will greatly accelerate the use of metagenomics to address critical aspects related to the detection and surveillance of plant pathogens in plant material and foodstuffs.},
}
@article {pmid33466668,
year = {2021},
author = {Eze, MO},
title = {Metagenome Analysis of a Hydrocarbon-Degrading Bacterial Consortium Reveals the Specific Roles of BTEX Biodegraders.},
journal = {Genes},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/genes12010098},
pmid = {33466668},
issn = {2073-4425},
support = {2017561//Department of Education, Employment and Workplace Relations, Australian Government/ ; 91731339//Deutscher Akademischer Austauschdienst/ ; },
abstract = {Environmental contamination by petroleum hydrocarbons is of concern due to the carcinogenicity and neurotoxicity of these compounds. Successful bioremediation of organic contaminants requires bacterial populations with degradative capacity for these contaminants. Through successive enrichment of microorganisms from a petroleum-contaminated soil using diesel fuel as the sole carbon and energy source, we successfully isolated a bacterial consortium that can degrade diesel fuel hydrocarbons. Metagenome analysis revealed the specific roles of different microbial populations involved in the degradation of benzene, toluene, ethylbenzene and xylene (BTEX), and the metabolic pathways involved in these reactions. One hundred and five putative coding DNA sequences were identified as responsible for both the activation of BTEX and central metabolism (ring-cleavage) of catechol and alkylcatechols during BTEX degradation. The majority of the Coding DNA sequences (CDSs) were affiliated to Acidocella, which was also the dominant bacterial genus in the consortium. The inoculation of diesel fuel contaminated soils with the consortium resulted in approximately 70% hydrocarbon biodegradation, indicating the potential of the consortium for environmental remediation of petroleum hydrocarbons.},
}
@article {pmid33466640,
year = {2021},
author = {Kovács, R and Nagy, F and Tóth, Z and Forgács, L and Tóth, L and Váradi, G and Tóth, GK and Vadászi, K and Borman, AM and Majoros, L and Galgóczy, L},
title = {The Neosartorya fischeri Antifungal Protein 2 (NFAP2): A New Potential Weapon against Multidrug-Resistant Candida auris Biofilms.},
journal = {International journal of molecular sciences},
volume = {22},
number = {2},
pages = {},
doi = {10.3390/ijms22020771},
pmid = {33466640},
issn = {1422-0067},
support = {EFOP-3.6.3-VEKOP-16-2017-00009//Ministry of Human Capacities/ ; FEMS-GO-2019-502//FEMS/ ; ÚNKP-19-3//Ministry of Human Capacities/ ; ÚNKP-20-3//Ministry of Human Capacities/ ; ANN 131341//Hungarian National Research, Development and Innovation (NKFIH) Office/ ; OTKA Bridging Fund//Hungarian National Research, Development and Innovation (NKFIH) Office/ ; TKP-2020//the Ministry of Human Capacities/ ; GINOP-2.3.2-15-2016-00014//Hungarian National Research, Development and Innovation (NKFIH) Office/ ; GINOP-2.3.4-15-2020-00008//Hungarian National Research, Development and Innovation (NKFIH) Office/ ; ÚNKP-20-5//New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund/ ; },
abstract = {Candida auris is a potential multidrug-resistant pathogen able to persist on indwelling devices as a biofilm, which serve as a source of catheter-associated infections. Neosartorya fischeri antifungal protein 2 (NFAP2) is a cysteine-rich, cationic protein with potent anti-Candida activity. We studied the in vitro activity of NFAP2 alone and in combination with fluconazole, amphotericin B, anidulafungin, caspofungin, and micafungin against C. auris biofilms. The nature of interactions was assessed utilizing the fractional inhibitory concentration index (FICI), a Bliss independence model, and LIVE/DEAD viability assay. NFAP2 exerted synergy with all tested antifungals with FICIs ranging between 0.312-0.5, 0.155-0.5, 0.037-0.375, 0.064-0.375, and 0.064-0.375 for fluconazole, amphotericin B, anidulafungin, caspofungin, and micafungin, respectively. These results were confirmed using a Bliss model, where NFAP2 produced 17.54 μM2%, 2.16 μM2%, 33.31 μM2%, 10.72 μM2%, and 111.19 μM2% cumulative synergy log volume in combination with fluconazole, amphotericin B, anidulafungin, caspofungin, and micafungin, respectively. In addition, biofilms exposed to echinocandins (32 mg/L) showed significant cell death in the presence of NFAP2 (128 mg/L). Our study shows that NFAP2 displays strong potential as a novel antifungal compound in alternative therapies to combat C. auris biofilms.},
}
@article {pmid33466452,
year = {2021},
author = {Boyko, KM and Kryukova, MV and Petrovskaya, LE and Kryukova, EA and Nikolaeva, AY and Korzhenevsky, DA and Lomakina, GY and Novototskaya-Vlasova, KA and Rivkina, EM and Dolgikh, DA and Kirpichnikov, MP and Popov, VO},
title = {Structural and Biochemical Characterization of a Cold-Active PMGL3 Esterase with Unusual Oligomeric Structure.},
journal = {Biomolecules},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/biom11010057},
pmid = {33466452},
issn = {2218-273X},
support = {18-04-00491, 19-29-05003//Russian Foundation for Basic Research/ ; w/o number//Ministry of Science and Higher Education/ ; },
abstract = {The gene coding for a novel cold-active esterase PMGL3 was previously obtained from a Siberian permafrost metagenomic DNA library and expressed in Escherichia coli. We elucidated the 3D structure of the enzyme which belongs to the hormone-sensitive lipase (HSL) family. Similar to other bacterial HSLs, PMGL3 shares a canonical α/β hydrolase fold and is presumably a dimer in solution but, in addition to the dimer, it forms a tetrameric structure in a crystal and upon prolonged incubation at 4 °C. Detailed analysis demonstrated that the crystal tetramer of PMGL3 has a unique architecture compared to other known tetramers of the bacterial HSLs. To study the role of the specific residues comprising the tetramerization interface of PMGL3, several mutant variants were constructed. Size exclusion chromatography (SEC) analysis of D7N, E47Q, and K67A mutants demonstrated that they still contained a portion of tetrameric form after heat treatment, although its amount was significantly lower in D7N and K67A compared to the wild type. Moreover, the D7N and K67A mutants demonstrated a 40 and 60% increase in the half-life at 40 °C in comparison with the wild type protein. Km values of these mutants were similar to that of the wt PMGL3. However, the catalytic constants of the E47Q and K67A mutants were reduced by ~40%.},
}
@article {pmid33465647,
year = {2021},
author = {Zhou, L and Zhao, B and Ou, P and Zhang, W and Li, H and Yi, S and Zhuang, WQ},
title = {Core nitrogen cycle of biofoulant in full-scale anoxic &amp; oxic biofilm-membrane bioreactors treating textile wastewater.},
journal = {Bioresource technology},
volume = {325},
number = {},
pages = {124667},
doi = {10.1016/j.biortech.2021.124667},
pmid = {33465647},
issn = {1873-2976},
abstract = {Core nitrogen cycle within biofoulant in full-scale anoxic &amp; oxic biofilm-membrane bioreactor (bMBR) treating textile wastewater was investigated. Wastewater filtered through membrane with biofoulant had elevated NH4+-N and NO2--N concentrations corresponding to decreased NO3--N concentrations. Nevertheless, total nitrogen concentrations did not change significantly, indicating negligible nitrogen removal activities within biofoulant. Metagenomic analysis revealed a lack of genes, such as AmoCAB and Hao in biofoulant, indicating absence of nitrification or anammox populations. However, genes encoding complete pathway for dissimilatory nitrate reduction to ammonium (DNRA) were discovered in 15 species that also carry genes encoding both nitrate reductase and nitrite reductase. No specie contained all genes for complete denitrification pathway. High temperature, high C:N ratio, and anoxic conditions of textile wastewater could favorite microbes growth with DNRA pathway over those with canonical denitrification pathway. High dissolved oxygen concentrations could effectively inhibit DNRA to minimize ammonia concentration in the effluent.},
}
@article {pmid33465599,
year = {2021},
author = {Das, A},
title = {The relational genomics of cognitive function: A longitudinal study.},
journal = {Social science &amp; medicine (1982)},
volume = {270},
number = {},
pages = {113698},
doi = {10.1016/j.socscimed.2021.113698},
pmid = {33465599},
issn = {1873-5347},
abstract = {OBJECTIVES: Research in social genetics indicates a person's genome may influence outcomes of those in close relationships. Implications for cognitive function remain unexplored. The current study examined such &quot;metagenomic&quot; patterns among older U.S. couples.<br><br>METHODS: Data were from married or cohabiting couples in the 2006-2016 waves of the Health and Retirement Study, nationally representative of U.S. adults over 50. Measures included cognitive function as well as separate polygenic scores for cognition and for educational attainment. Analysis was through parallel process latent growth models.<br><br>RESULTS: Consistent with a recent &quot;genetic externalities&quot; conception, one partner's polygenic score for educational attainment was linked to the other's baseline levels of cognitive function. Contrary to relational moderation speculations, neither a partner's genetic scores nor educational attainment altered individual-level genetic influences.<br><br>DISCUSSION: Findings add to the growing evidence that transpersonal genetic influences in one's proximal context have substantively important implications. Research is needed on the role of non-partnership ties in channeling such effects. Implications for life course theory are discussed.},
}
@article {pmid33465548,
year = {2021},
author = {Nikoloudaki, O and Lemos Junior, WJF and Campanaro, S and Di Cagno, R and Gobbetti, M},
title = {Role prediction of Gram-negative species in the resistome of raw cow's milk.},
journal = {International journal of food microbiology},
volume = {340},
number = {},
pages = {109045},
doi = {10.1016/j.ijfoodmicro.2021.109045},
pmid = {33465548},
issn = {1879-3460},
abstract = {Extended use of antibiotics in dairy farming for therapeutic and prophylactic reasons, but also the higher prevalence of antibiotic resistant bacteria (ARB) in the farm environment raised the concern of consuming raw cow's milk and its derived products. The aim of this study was to predict by shotgun metagenomic analyses the presence of antibiotic resistance genes (ARGs) mainly correlated with Gram-negative bacteria in antibiotic residue free raw cow's milk derived exclusively from healthy animal from South Tyrol (Northern Italy), chosen as a model system. Assessment of shotgun metagenomic data of reconstructed scaffolds, revealed the existence of Pseudomonas spp. as the most abundant Gram-negative species in the raw cow's milk samples bearing ARGs. Besides, ARGs also linked to lactic acid bacteria such as Lactococcus sp. and Lactobacillus sp. ARGs correlated to microbiome found in milk samples conferred resistance towards aminoglycoside-streptothricin, beta-lactamase, macrolide, tetracycline, carbapenem, cephalosporin, penam, peptide, penem, fluoroquinolone, chloramphenicol and elfamycin antibiotics. Further bioinformatic processing included de-novo reassembly of all metagenomic sequences from all milk samples in one, to reconstruct metagenome assembled genomes (MAGs), which were further used to investigate mobile genetic elements (MGE). Analyses of the reconstructed MAGs showed that, MAG 9 (Pseudomonas sp1.) contained the oriT gene (origin of transfer gene) needed for transferring virulent factors. Although the presence of Pseudomonas is common in raw cow's milk, pasteurization treatment reduces their survivability. Nevertheless, attention should be paid on Pseudomonas spp. due to their intrinsic resistance to antibiotics and their capability of transferring virulent factors to other bacteria.},
}
@article {pmid33464408,
year = {2021},
author = {Wang, J and Liang, J and Li, Y and Tian, L and Wei, Y},
title = {Characterization of efficient xylanases from industrial-scale pulp and paper wastewater treatment microbiota.},
journal = {AMB Express},
volume = {11},
number = {1},
pages = {19},
pmid = {33464408},
issn = {2191-0855},
support = {31800079//National Natural Science Foundation of China/ ; },
abstract = {Xylanases are widely used enzymes in the food, textile, and paper industries. Most efficient xylanases have been identified from lignocellulose-degrading microbiota, such as the microbiota of the cow rumen and the termite hindgut. Xylanase genes from efficient pulp and paper wastewater treatment (PPWT) microbiota have been previously recovered by metagenomics, assigning most of the xylanase genes to the GH10 family. In this study, a total of 40 GH10 family xylanase genes derived from a certain PPWT microbiota were cloned and expressed in Escherichia coli BL21 (DE3). Among these xylanase genes, 14 showed xylanase activity on beechwood substrate. Two of these, PW-xyl9 and PW-xyl37, showed high activities, and were purified to evaluate their xylanase properties. Values of optimal pH and temperature for PW-xyl9 were pH 7 and 60 ℃, respectively, while those for PW-xyl37 were pH 7 and 55 ℃, respectively; their specific xylanase activities under optimal conditions were 470.1 U/mg protein and 113.7 U/mg protein, respectively. Furthermore, the Km values of PW-xyl9 and PW-xyl37 were determined as 8.02 and 18.8 g/L, respectively. The characterization of these two xylanases paves the way for potential application in future pulp and paper production and other industries, indicating that PPWT microbiota has been an undiscovered reservoir of efficient lignocellulase genes. This study demonstrates that a metagenomic approach has the potential to screen efficient xylanases of uncultured microorganisms from lignocellulose-degrading microbiota. In a similar way, other efficient lignocellulase genes might be identified from PPWT treatment microbiota in the future.},
}
@article {pmid33463854,
year = {2020},
author = {Furey, PC and Lee, SS and Clemans, DL},
title = {Substratum-associated microbiota.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {92},
number = {10},
pages = {1629-1648},
doi = {10.1002/wer.1410},
pmid = {33463854},
issn = {1554-7531},
mesh = {*Cyanobacteria ; Ecology ; Fresh Water ; Metagenomics ; *Microbiota ; },
abstract = {Highlights of new, interesting, and emerging research findings on substratum-associated microbiota covered from a survey of 2019 literature from primarily freshwaters provide insight into research trends of interest to the Water Environment Federation and others interested in benthic, aquatic environments. Coverage of topics on bottom-associated or attached algae and cyanobacteria, though not comprehensive, includes new methods, taxa new-to-science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, and bloom-forming and harmful algae. Coverage of bacteria, also not comprehensive, focuses on the ecology of benthic biofilms and microbial communities, along with the ecology of microbes like Caulobacter crescentus, Rhodobacter, and other freshwater microbial species. Bacterial topics covered also include metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Readers may use this literature review to learn about or renew their interest in the recent advances and discoveries regarding substratum-associated microbiota. PRACTITIONER POINTS: This review of literature from 2019 on substratum-associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters. Coverage of algae and cyanobacteria includes findings on new methods, taxa new to science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, bloom-forming and harmful algae. Coverage of bacteria includes findings on ecology of benthic biofilms and microbial communities, the ecology of microbes, metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Highlights of new, noteworthy and emerging topics build on those from 2018 and will be of relevance to the Water Environment Federation and others interested in benthic, aquatic environments.},
}
@article {pmid33463503,
year = {2020},
author = {Wang, Y and Lu, H and Shao, R and Wang, W},
title = {[Clinical characteristics analysis of patients with pneumonia infected by Chlamydia psittaci].},
journal = {Zhonghua wei zhong bing ji jiu yi xue},
volume = {32},
number = {11},
pages = {1388-1390},
doi = {10.3760/cma.j.cn121430-20200408-00259},
pmid = {33463503},
issn = {2095-4352},
mesh = {*Chlamydophila psittaci ; Cough ; Dyspnea ; Humans ; *Pneumonia ; Retrospective Studies ; },
abstract = {OBJECTIVE: To explore the clinical characteristics of pneumonia infected by Chlamydophila psittaci (C. psittaci).<br><br>METHODS: A retrospective analysis was performed on 3 cases of C. psittaci pneumonia admitted to People's Hospital of Tongling City from July 2019 to January 2020. The patients' contact history, clinical manifestations, laboratory examination, imaging characteristics and evolution, etiology, treatment process and outcome were analyzed, so as to provide experience for the diagnosis and prevention of C. psittaci pneumonia.<br><br>RESULTS: The 3 patients had been infected through pet or zoonotic exposures. All symptoms included high fever (body temperature > 39 centigrade), cough, sputum, chest tightness and dyspnea. The disease progressed rapidly, with severe acute respiratory distress syndrome (ARDS) and shock as the main manifestations, but the damages to the heart, liver and kidney were mild. Laboratory tests showed that C-reactive protein (CRP, all > 200 mg/L) and neutrophil proportion (Neut%, > 0.90) were significantly increased, while white blood cell count (WBC) and procalcitonin (PCT) were not significantly increased. Chest computed tomography (CT) showed inflammatory infiltration with interstitial changes, either unilateral or bilateral. Chest X-ray showed large areas of inflammatory infiltrations, fan-shaped or wedge-shaped to the edge of pleura. After 7 days of treatment, the bedside computed X-ray (CR) showed absorption of infiltration. After 11-13 days, the CT reexamination indicated lung infection was basically absorbed. Metagenomic next-generation sequencing (mNGS) confirmed the presence of C. psittaci in patients' sputum. It was sensitive to quinolones and tetracyclines. The patients' body temperature dropped to normal after 2-3 days of antibiotics, and all patients were extubated and transferred to normal ward 10 days later. The total course of illness was 20-30 days.<br><br>CONCLUSIONS: The patients with C. psittaci pneumonia are critically ill, and clinical manifestations of moderate to severe ARDS and shock are common. Early diagnosis depends on mNGS, and reasonable treatment is important for prognosis.},
}
@article {pmid33462601,
year = {2021},
author = {Garg, SG and Kapust, N and Lin, W and Knopp, M and Tria, FDK and Nelson-Sathi, S and Gould, SB and Fan, L and Zhu, R and Zhang, C and Martin, WF},
title = {Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea.},
journal = {Genome biology and evolution},
volume = {13},
number = {1},
pages = {},
doi = {10.1093/gbe/evaa238},
pmid = {33462601},
issn = {1759-6653},
abstract = {Metagenomic studies permit the exploration of microbial diversity in a defined habitat, and binning procedures enable phylogenomic analyses, taxon description, and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here, we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: These proteins do not share common evolutionary histories to the same extent as pure culture genomes do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.},
}
@article {pmid33462508,
year = {2021},
author = {Olm, MR and Crits-Christoph, A and Bouma-Gregson, K and Firek, BA and Morowitz, MJ and Banfield, JF},
title = {inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {33462508},
issn = {1546-1696},
support = {DGE 1106400//National Science Foundation (NSF)/ ; DGE1106400//National Science Foundation (NSF)/ ; APSF-2012-10-05//Alfred P. Sloan Foundation/ ; RAI092531A//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; },
abstract = {Coexisting microbial cells of the same species often exhibit genetic variation that can affect phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a program that uses metagenomic paired reads to profile intra-population genetic diversity (microdiversity) across whole genomes and compares microbial populations in a microdiversity-aware manner, greatly increasing the accuracy of genomic comparisons when benchmarked against existing methods. We use inStrain to profile >1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born by cesarean section harbor Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital rather than maternal microbiomes. Genomic loci that show diversity in individual infants include variants found between other infants, possibly reflecting inoculation from diverse hospital-associated sources. inStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison.},
}
@article {pmid33462312,
year = {2021},
author = {Blifernez-Klassen, O and Klassen, V and Wibberg, D and Cebeci, E and Henke, C and Rückert, C and Chaudhari, S and Rupp, O and Blom, J and Winkler, A and Al-Dilaimi, A and Goesmann, A and Sczyrba, A and Kalinowski, J and Bräutigam, A and Kruse, O},
title = {Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1726},
pmid = {33462312},
issn = {2045-2322},
support = {311956//European Union Seventh Framework/ ; 311956//European Union Seventh Framework/ ; 311956//European Union Seventh Framework/ ; 031A533//Bundesministerium für Bildung, Wissenschaft und Forschung/ ; 031A533//Bundesministerium für Bildung, Wissenschaft und Forschung/ ; 031A533//Bundesministerium für Bildung, Wissenschaft und Forschung/ ; },
abstract = {Bacteria occupy all major ecosystems and maintain an intensive relationship to the eukaryotes, developing together into complex biomes (i.e., phycosphere and rhizosphere). Interactions between eukaryotes and bacteria range from cooperative to competitive, with the associated microorganisms affecting their host`s development, growth and health. Since the advent of non-culture dependent analytical techniques such as metagenome sequencing, consortia have been described at the phylogenetic level but rarely functionally. Multifaceted analysis of the microbial consortium of the ancient phytoplankton Botryococcus as an attractive model food web revealed that its all abundant bacterial members belong to a niche of biotin auxotrophs, essentially depending on the microalga. In addition, hydrocarbonoclastic bacteria without vitamin auxotrophies seem adversely to affect the algal cell morphology. Synthetic rearrangement of a minimal community consisting of an alga, a mutualistic and a parasitic bacteria underpins the model of a eukaryote that maintains its own mutualistic microbial community to control its surrounding biosphere. This model of coexistence, potentially useful for defense against invaders by a eukaryotic host could represent ecologically relevant interactions that cross species boundaries. Metabolic and system reconstruction is an opportunity to unravel the relationships within the consortia and provide a blueprint for the construction of mutually beneficial synthetic ecosystems.},
}
@article {pmid33462272,
year = {2021},
author = {Jacobson, DK and Honap, TP and Ozga, AT and Meda, N and Kagoné, TS and Carabin, H and Spicer, P and Tito, RY and Obregon-Tito, AJ and Reyes, LM and Troncoso-Corzo, L and Guija-Poma, E and Sankaranarayanan, K and Lewis, CM},
title = {Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1724},
pmid = {33462272},
issn = {2045-2322},
support = {GM089886/NH/NIH HHS/United States ; 1925579//National Science Foundation/ ; },
abstract = {High taxonomic diversity in non-industrial human gut microbiomes is often interpreted as beneficial; however, it is unclear if taxonomic diversity engenders ecological resilience (i.e. community stability and metabolic continuity). We estimate resilience through genus and species-level richness, phylogenetic diversity, and evenness in short-chain fatty acid (SCFA) production among a global gut metagenome panel of 12 populations (n = 451) representing industrial and non-industrial lifestyles, including novel metagenomic data from Burkina Faso (n = 90). We observe significantly higher genus-level resilience in non-industrial populations, while SCFA production in industrial populations is driven by a few phylogenetically closely related species (belonging to Bacteroides and Clostridium), meaning industrial microbiomes have low resilience potential. Additionally, database bias obfuscates resilience estimates, as we were 2-5 times more likely to identify SCFA-encoding species in industrial microbiomes compared to non-industrial. Overall, we find high phylogenetic diversity, richness, and evenness of bacteria encoding SCFAs in non-industrial gut microbiomes, signaling high potential for resilience in SCFA production, despite database biases that limit metagenomic analysis of non-industrial populations.},
}
@article {pmid33461660,
year = {2021},
author = {Urban, L and Holzer, A and Baronas, JJ and Hall, MB and Braeuninger-Weimer, P and Scherm, MJ and Kunz, DJ and Perera, SN and Martin-Herranz, DE and Tipper, ET and Salter, SJ and Stammnitz, MR},
title = {Freshwater monitoring by nanopore sequencing.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
doi = {10.7554/eLife.61504},
pmid = {33461660},
issn = {2050-084X},
support = {Graduate Student Fellowship//Gates Cambridge Trust/ ; OPP1144//Bill and Melinda Gates Foundation/ ; OpenPlant Fund (BBSRC BB/L014130/1)/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Public Engagement Starter Grant (RCUK Catalyst Seed Fund)//University of Cambridge/ ; Graduate Student Fellowship//European Bioinformatics Institute/ ; Graduate Student Fellowship (203828/Z/16/A, 203828/Z/16/Z)/WT_/Wellcome Trust/United Kingdom ; Graduate Student Fellowship (102453/Z/13/Z)/WT_/Wellcome Trust/United Kingdom ; Graduate Student Fellowship//Oliver Gatty Studentship/ ; Standard Grant (NE/P011659/1)//Natural Environment Research Council/ ; },
abstract = {While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.},
}
@article {pmid33461494,
year = {2021},
author = {Dhungel, E and Mreyoud, Y and Gwak, HJ and Rajeh, A and Rho, M and Ahn, TH},
title = {MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {25},
pmid = {33461494},
issn = {1471-2105},
support = {1564894//National Science Foundation/ ; },
abstract = {BACKGROUND: Diverse microbiome communities drive biogeochemical processes and evolution of animals in their ecosystems. Many microbiome projects have demonstrated the power of using metagenomics to understand the structures and factors influencing the function of the microbiomes in their environments. In order to characterize the effects from microbiome composition for human health, diseases, and even ecosystems, one must first understand the relationship of microbes and their environment in different samples. Running machine learning model with metagenomic sequencing data is encouraged for this purpose, but it is not an easy task to make an appropriate machine learning model for all diverse metagenomic datasets.<br><br>RESULTS: We introduce MegaR, an R Shiny package and web application, to build an unbiased machine learning model effortlessly with interactive visual analysis. The MegaR employs taxonomic profiles from either whole metagenome sequencing or 16S rRNA sequencing data to develop machine learning models and classify the samples into two or more categories. It provides various options for model fine tuning throughout the analysis pipeline such as data processing, multiple machine learning techniques, model validation, and unknown sample prediction that can be used to achieve the highest prediction accuracy possible for any given dataset while still maintaining a user-friendly experience.<br><br>CONCLUSIONS: Metagenomic sample classification and phenotype prediction is important particularly when it applies to a diagnostic method for identifying and predicting microbe-related human diseases. MegaR provides various interactive visualizations for user to build an accurate machine-learning model without difficulty. Unknown sample prediction with a properly trained model using MegaR will enhance researchers to identify the sample property in a fast turnaround time.},
}
@article {pmid33454531,
year = {2021},
author = {Lu, H and Wang, J and Huang, L and Wang, X and Zhou, J and Wang, J},
title = {Effect of immobilized anthraquinone-2-sulfonate on antibiotic resistance genes and microbial community in biofilms of anaerobic reactors.},
journal = {Journal of environmental management},
volume = {282},
number = {},
pages = {111967},
doi = {10.1016/j.jenvman.2021.111967},
pmid = {33454531},
issn = {1095-8630},
abstract = {Quinone compounds could significantly accelerate anaerobic biotransformation of refractory pollutants. However, the effect of quinone compounds application on the propagation of antibiotic resistance genes (ARGs) in the bio-treatment of these pollutants-containing wastewater is not available. In this study, the catalytic performance of anthraquinone-2-sulfonate immobilized on polyurethane foam (AQS-PUF), changes of ARGs, mobile gene elements (MGEs) and microbial community structure attached on AQS-PUF and PUF in the up-flow anaerobic bioreactors were investigated. The results showed that AQS-PUF could significantly accelerate the decolorization of azo dye RR X-3B. Meanwhile, metagenomics analysis showed that the total absolute abundance of ARGs increased in the presence of the immobilized AQS. Among ARGs, the number of the efflux pump-encoding ARGs in the biofilm of AQS-PUF accounted for 35.7% of the total ARGs, which was slightly higher than that of PUF (32.1%) due to the presence of the immobilized AQS. The relative abundances of ARGs conferring resistance to MLS (macrolide, lincosamide and streptogramin), tetracycline and sulfonamide, which were deeply concerned, reduced 10%, 21.7% and 7.3% in the presence of the immobilized AQS, respectively. Moreover, the immobilized AQS resulted in the decreased relative abundance of plasmids, transposons and class I integrons. Among the detected 31 ARG subtypes located in MGEs, the relative abundances of only lnuF, msrE and mphD in the biofilm of AQS-PUF were over 2-fold higher compared with those in the biofilm of PUF. However, the three ARGs and their host Gammaproteobacteria was not dominant in microbial community. The relative abundances of more ARGs including MLS (lnuB and EreA), tetracycline (tetH) resistance genes located in MGEs decreased, which was attributed to the decreased relative abundance of their hosts. These studies showed that the addition of the immobilized AQS (around 0.25 mM) had a beneficial effect on reducing the spread of ARGs during dyeing wastewater bio-treatment.},
}
@article {pmid33454444,
year = {2021},
author = {Sharma, P and Tripathi, S and Chandra, R},
title = {Metagenomic analysis for profiling of microbial communities and tolerance in metal-polluted pulp and paper industry wastewater.},
journal = {Bioresource technology},
volume = {324},
number = {},
pages = {124681},
doi = {10.1016/j.biortech.2021.124681},
pmid = {33454444},
issn = {1873-2976},
abstract = {This work aimed to study the profiling and efficiency of microbial communities and their abundance in the pulp and paper industry wastewater, which contained toxic metals, high biological oxygen demands, chemical oxygen demand, and ions contents. Sequence alignment of the 16S rRNA V3-V4 variable region zone with the Illumina MiSeq framework revealed 25356 operating taxonomical units (OTUs) derived from the wastewater sample. The major phyla identified in wastewater were Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Actinobacteria, Spirochetes, Patesibacteria, Acidobacteria, and others including unknown microbes. The study showed the function of microbial communities essential for the oxidation and detoxifying of complex contaminants and design of effective remediation techniques for the re-use of polluted wastewater. Findings demonstrated that the ability of different classes of microbes to adapt and survive in metal-polluted wastewater irrespective of their relative distribution, as well as further attention can be provided to its use in the bioremediation process.},
}
@article {pmid33460896,
year = {2021},
author = {Gao, Y and Du, J and Bahar, MM and Wang, H and Subashchandrabose, S and Duan, L and Yang, X and Megharaj, M and Zhao, Q and Zhang, W and Liu, Y and Wang, J and Naidu, R},
title = {Metagenomics analysis identifies nitrogen metabolic pathway in bioremediation of diesel contaminated soil.},
journal = {Chemosphere},
volume = {271},
number = {},
pages = {129566},
doi = {10.1016/j.chemosphere.2021.129566},
pmid = {33460896},
issn = {1879-1298},
abstract = {Nitrogen amendment is known to effectively enhance the bioremediation of hydrocarbon-contaminated soil, but the nitrogen metabolism in this process is not well understood. To unravel the nitrogen metabolic pathway(s) of diesel contaminated soil, six types of nitrogen sources were added to the diesel contaminated soil. Changes in microbial community and soil enzyme genes were investigated by metagenomics analysis and chemical analysis through a 30-day incubation study. The results showed that ammonium based nitrogen sources significantly accelerated the degradation of total petroleum hydrocarbon (TPH) (79-81%) compared to the control treatment (38%) and other non-ammonium based nitrogen amendments (43-57%). Different types of nitrogen sources could dramatically change the microbial community structure and soil enzyme gene abundance. Proteobacteria and Actinobacteria were identified as the two dominant phyla in the remediation of diesel contaminated soil. Metagenomics analysis revealed that the preferred metabolic pathway of nitrogen was from ammonium to glutamate via glutamine, and the enzymes governing this transformation were glutamine synthetase and glutamate synthetase; while in nitrate based amendment, the conversion from nitrite to ammonium was restrained by the low abundance of nitrite reductase enzyme and therefore retarded the TPH degradation rate. It is concluded that during the process of nitrogen enhanced bioremediation, the most efficient nitrogen cycling direction was from ammonium to glutamine, then to glutamate, and finally joined with carbon metabolism after transforming to 2-oxoglutarate.},
}
@article {pmid33460836,
year = {2021},
author = {Nie, S and Zhang, Z and Mo, S and Li, J and He, S and Kashif, M and Liang, Z and Shen, P and Yan, B and Jiang, C},
title = {Desulfobacterales stimulates nitrate reduction in the mangrove ecosystem of a subtropical gulf.},
journal = {The Science of the total environment},
volume = {769},
number = {},
pages = {144562},
doi = {10.1016/j.scitotenv.2020.144562},
pmid = {33460836},
issn = {1879-1026},
abstract = {The amount of nitrogen compounds discharged into the natural environment has increased drastically due to frequent human activities and led to worsening pollution. The mangrove ecosystem can remove nitrogen pollution, in this regard, few studies had focused on the relationship among nitrogen cycling genes, environmental factors, and taxonomic composition. In this study, shotgun metagenomic sequencing and quantitative polymerase chain reaction were used to understand the nitrogen cycle in the subtropical mangrove ecosystem in the Beibu Gulf of China. Eight nitrogen cycling pathways were annotated. Nitrogen metabolism activities were significantly higher in the wet season than those in the dry season. The most abundant genes were those related to the synthesis and degradation of organic nitrogen, followed by the genes involved in nitrate reduction (denitrification, dissimilation/assimilation nitrate reduction). Furthermore, dissimilation nitrate reduction was the main nitrate reduction pathway. Desulfobacterales plays an important role in nitrogen cycling and contributes 12% of the genes of nitrogen pathways on average; as such, a strong coupling relationship exists among nitrogen cycling, sulfur cycling, and carbon cycling in the mangrove ecosystem. Nitrogen pollution in the mangrove wetland can be efficiently alleviated by nitrate reduction of Desulfobacterales. Nevertheless, only 50% of genes can be matched among the known species, suggesting that many unknown microorganisms in the mangrove ecosystem can perform nitrogen cycling. Total phosphorus, available iron, and total organic carbon are the key environmental factors that influence the distribution of nitrogen cycling genes, related pathways, and the taxonomic composition. Our study clearly illustrates how the mangrove ecosystem mitigates nitrogen pollution through Desulfobacterales. This finding could provide a research reference for the whole nitrogen cycling in the mangrove ecosystem.},
}
@article {pmid33460821,
year = {2021},
author = {Meng, D and Mukhitov, N and Neitzey, D and Lucht, M and Schaak, DD and Voigt, CA},
title = {Rapid and simultaneous screening of pathway designs and chassis organisms, applied to engineered living materials.},
journal = {Metabolic engineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymben.2021.01.006},
pmid = {33460821},
issn = {1096-7184},
abstract = {Achieving a high product titer through pathway optimization often requires screening many combinations of enzymes and genetic parts. Typically, a library is screened in a single chassis that is a model or production organism. Here, we present a technique where the library is first introduced into B. subtilis XPORT, which has the ability to transfer the DNA to many Gram-positive species using an inducible integrated conjugated element (ICE). This approach is demonstrated using a two-gene pathway that converts tyrosine to melanin, a pigment biopolymer that can serve as a protective coating. A library of 18 pathway variants is conjugated by XPORT into 18 species, including those isolated from soil and industrial contaminants. The resulting 324 strains are screened and the highest titer is 1.2 g/L in B. amyloliquefaciens BT16. The strains were evaluated as co-cultures in an industrial process to make mycelia-grown bulk materials, where the bacteria need to be productive in a stressful, spatially non-uniform and dynamic environment. B. subtilis 3A35 is found to perform well under these conditions and make melanin in the material, which can be seen visually. This approach enables the simultaneous screening of genetic designs and chassis during the build step of metabolic engineering.},
}
@article {pmid33460770,
year = {2021},
author = {Aymé, L and Hébert, A and Henrissat, B and Lombard, V and Franche, N and Perret, S and Jourdier, E and Heiss-Blanquet, S},
title = {Characterization of three bacterial glycoside hydrolase family 9 endoglucanases with different modular architectures isolated from a compost metagenome.},
journal = {Biochimica et biophysica acta. General subjects},
volume = {},
number = {},
pages = {129848},
doi = {10.1016/j.bbagen.2021.129848},
pmid = {33460770},
issn = {1872-8006},
abstract = {BACKGROUND: Environmental bacteria express a wide diversity of glycoside hydrolases (GH). Screening and characterization of GH from metagenomic sources provides an insight into biomass degradation strategies of non-cultivated prokaryotes.<br><br>METHODS: In the present report, we screened a compost metagenome for lignocellulolytic activities and identified six genes encoding enzymes belonging to family GH9 (GH9a-f). Three of these enzymes (GH9b, GH9d and GH9e) were successfully expressed and characterized.<br><br>RESULTS: A phylogenetic analysis of the catalytic domain of pro- and eukaryotic GH9 enzymes suggested the existence of two major subgroups. Bacterial GH9s displayed a wide variety of modular architectures and those harboring an N-terminal Ig-like domain, such as GH9b and GH9d, segregated from the remainder. We purified and characterized GH9 endoglucanases from both subgroups and examined their stabilities, substrate specificities and product profiles. GH9e exhibited an original hydrolysis pattern, liberating an elevated proportion of oligosaccharides longer than cellobiose. All of the enzymes exhibited processive behavior and a synergistic action on crystalline cellulose. Synergy was also evidenced between GH9d and a GH48 enzyme identified from the same metagenome.<br><br>CONCLUSIONS: The characterized GH9 enzymes displayed different modular architectures and distinct substrate and product profiles. The presence of a cellulose binding domain was shown to be necessary for binding and digestion of insoluble cellulosic substrates, but not for processivity.<br><br>GENERAL SIGNIFICANCE: The identification of six GH9 enzymes from a compost metagenome and the functional variety of three characterized members highlight the importance of this enzyme family in bacterial biomass deconstruction.},
}
@article {pmid33459951,
year = {2021},
author = {Martin, C and Stebbins, B and Ajmani, A and Comendul, A and Hamner, S and Hasan, NA and Colwell, R and Ford, T},
title = {Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater.},
journal = {Ecotoxicology (London, England)},
volume = {},
number = {},
pages = {},
pmid = {33459951},
issn = {1573-3017},
abstract = {In-depth studies of the microbiome and mobile resistome profile of different environments is central to understanding the role of the environment in antimicrobial resistance (AMR), which is one of the urgent threats to global public health. In this study, we demonstrated the use of a rapid (and easily portable) sequencing approach coupled with user-friendly bioinformatics tools, the MinION (Oxford Nanopore Technologies), on the evaluation of the microbial as well as mobile metal and antibiotic resistome profile of semi-rural wastewater. A total of 20 unique phyla, 43 classes, 227 genera, and 469 species were identified in samples collected from the Amherst Wastewater Treatment Plant, both from primary and secondary treated wastewater. Alpha diversity indices indicated that primary samples were significantly richer and more microbially diverse than secondary samples. A total of 1041 ARGs, 68 MRGs, and 17 MGEs were detected in this study. There were more classes of AMR genes in primary than secondary wastewater, but in both cases multidrug, beta-lactam and peptide AMR predominated. Of note, OXA β-lactamases, some of which are also carbapenemases, were enriched in secondary samples. Metal resistance genes against arsenic, copper, zinc and molybdenum were the dominant MRGs in the majority of the samples. A larger proportion of resistome genes were located in chromosome-derived sequences except for mobilome genes, which were predominantly located in plasmid-derived sequences. Genetic elements related to transposase were the most common MGEs in all samples. Mobile or MGE/plasmid-associated resistome genes that confer resistance to last resort antimicrobials such as carbapenems and colistin were detected in most samples. Worryingly, several of these potentially transferable genes were found to be carried by clinically-relevant hosts including pathogenic bacterial species in the orders Aeromonadales, Clostridiales, Enterobacterales and Pseudomonadales. This study demonstrated that the MinION can be used as a metagenomics approach to evaluate the microbiome, resistome, and mobilome profile of primary and secondary wastewater.},
}
@article {pmid33459515,
year = {2020},
author = {Bertagnolli, AD and Konstantinidis, KT and Stewart, FJ},
title = {Non-denitrifier nitrous oxide reductases dominate marine biomes.},
journal = {Environmental microbiology reports},
volume = {12},
number = {6},
pages = {681-692},
doi = {10.1111/1758-2229.12879},
pmid = {33459515},
issn = {1758-2229},
support = {//National Science Foundation/ ; },
abstract = {Microbial enzymes often occur as distinct variants that share the same substrate but differ in substrate affinity, sensitivity to environmental conditions, or phylogenetic ancestry. Determining where variants occur in the environment helps identify thresholds that constrain microbial cycling of key chemicals, including the greenhouse gas nitrous oxide (N2O). To understand the enzymatic basis of N2O cycling in the ocean, we mined metagenomes to characterize genes encoding bacterial nitrous oxide reductase (NosZ) catalyzing N2O reduction to N2. We examined data sets from diverse biomes but focused primarily on those from oxygen minimum zones where N2O levels are often elevated. With few exceptions, marine nosZ data sets were dominated by 'atypical' clade II gene variants. Atypical nosZ has been associated with low oxygen, enhanced N2O affinity, and organisms lacking enzymes for complete denitrification, i.e., non-denitrifiers. Atypical nosZ often occurred in metagenome-assembled genomes (MAGs) with nitrate or nitrite respiration genes, although MAGs with genes for complete denitrification were rare. We identified atypical nosZ in several taxa not previously associated with N2O consumption, in addition to known N2O-associated groups. The data suggest that marine environments generally select for high N2O-scavenging ability across diverse taxa and have implications for how N2O concentration may affect N2O removal rates.},
}
@article {pmid33458619,
year = {2021},
author = {Sobat, M and Asad, S and Kabiri, M and Mehrshad, M},
title = {Metagenomic discovery and functional validation of L-asparaginases with anti-leukemic effect from the Caspian Sea.},
journal = {iScience},
volume = {24},
number = {1},
pages = {101973},
pmid = {33458619},
issn = {2589-0042},
abstract = {By screening 27,000 publicly available prokaryotic genomes, we recovered ca. 6300 type I and ca. 5200 type II putative L-asparaginase highlighting the vast potential of prokaryotes. Caspian water with similar salt composition to the human serum was targeted for in silico L-asparaginase screening. We screened ca. three million predicted genes of its assembled metagenomes that resulted in annotation of 87 putative L-asparaginase genes. The L-asparagine hydrolysis was experimentally confirmed by synthesizing and cloning three selected genes in E. coli. Catalytic parameters of the purified enzymes were determined to be among the most desirable reported values. Two recombinant enzymes represented remarkable anti-proliferative activity (IC50 <1IU/ml) against leukemia cell line Jurkat while no cytotoxic effect on human erythrocytes or human umbilical vein endothelial cells was detected. Similar salinity and ionic concentration of the Caspian water to the human serum highlights the potential of secretory L-asparaginases recovered from these metagenomes as potential treatment agents.},
}
@article {pmid33457168,
year = {2021},
author = {Chandra, A and Gaur, V and Tripathi, P},
title = {Microbiome analysis of rhizospheres of plant and winter-initiated ratoon crops of sugarcane grown in sub-tropical India: utility to improve ratoon crop productivity.},
journal = {3 Biotech},
volume = {11},
number = {1},
pages = {34},
pmid = {33457168},
issn = {2190-572X},
abstract = {One plant and one to two ratoon crops are the predominant patterns of sugarcane cultivation in sub-tropical part of India. Despite high agricultural inputs, yield of ratoon crop gets dwindled in the subsequent years. The microbial community, particularly bacteria and fungi, in the rhizosphere and their interaction with the root system, in general influences plant productivity. For the present study, an early maturing sugarcane variety (CoLk 94184), was used to establish plant and winter-initiated ratoon crops in 2016-2018. Soils pertaining to both plant and ratoon rhizospheres were subjected to biochemical analysis, microbial DNA isolation and high-throughput sequencing of 16S rRNA genes to assess the microbial diversity and associated characteristics impacting cane yield. Although alpha diversity of bacterial community was observed high in the soils of both plant and ratoon crops, the species richness/diversity was more in plant crop. Bacterial community structure in the rhizosphere of plant crop was predominantly consisted of phyla Actinobacteria (35.68%), Gemmatimonadetes (29.26%), Chloroflexi (26.73%) and Proteobacteria (16.68%), while ratoon rhizosphere revealed dominance of Acidobacteria (20.77%) and Bacteroidetes (10.7%). Though studies revealed the presence of rich bacterial community in the rhizospheres of both plant and ratoon crops of sugarcane, dominance of Acidobacteria and meager proportion of Actinobacteria and Proteobacteria in ratoon crop possibly limited its productivity. Along with high total phenols (7.27 mg/g dry wt), ratoon crop depicted less active root system as revealed by scanning electron microscopy. Dominance of thermophilic bacterial phyla Chloroflexi and Gemmatimonadetes which was observed in sugarcane rhizosphere supports better crop growth in drought. However, management of soil microbial community is required to improve the ratoon crop productivity.},
}
@article {pmid33455775,
year = {2021},
author = {Peng, C and Sun, Z and Sun, Y and Ma, T and Li, W and Zhang, H},
title = {Characterization and association of bacterial communities and nonvolatile components in spontaneously fermented cow milk at different geographical distances.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2020-19303},
pmid = {33455775},
issn = {1525-3198},
abstract = {In the ecosystem of spontaneously fermented cow milk, the characteristics and relationship of bacterial communities and nonvolatile components at different scales of geographical distances (provincial, county, and village levels) are unclear. Here, 25 sampling sites from Xin Jiang and Tibet, 2 provinces of China, were selected based on the distribution of spontaneously fermented cow milk and used for metagenomic and metabolomic analysis. At the provincial geographical distance, the same predominant species, Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus, were detected in Xin Jiang and Tibet. Further, the richness of the bacterial composition of samples from Tibet was higher than those from Xin Jiang; specifically, at the species level, 28 species were identified in Tibet samples but only 7 species in Xin Jiang samples. At the provincial geographical level, we detected significant differences in bacterial structure, shown in principal coordinate analysis plots, and significant differences (Simpson index) in bacterial diversity were also detected. However, at the county and village levels, no significant differences were detected in bacterial communities and diversity, but a difference in bacterial compositions was detectable. This indicates that bacterial communities and diversity of spontaneously fermented milk dissimilarity significantly increased with geographic distance. For the nonvolatile component profiles, the partial least squares discriminant analysis plot (R2Y > 0.5 and Q2 > 0.5 for the goodness-of-fit and predictive ability parameter, respectively) showed that samples from different geographical distances (provincial, county, and village) were all separated, which indicated that all the discriminations in nonvolatile components profiles were from different geographical distances. Investigating relationships between lactic acid bacteria and discriminatory nonvolatile components at the county level showed that 9 species were positively correlated with 16 discriminatory nonvolatile components, all species with low abundance rather than the predominant species L. delbrueckii ssp. bulgaricus and Strep. thermophilus, which indicates the importance of the selection of autochthonous nonpredominant bacteria.},
}
@article {pmid33455430,
year = {2021},
author = {Zotta, T and Ricciardi, A and Condelli, N and Parente, E},
title = {Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/10408398.2020.1870927},
pmid = {33455430},
issn = {1549-7852},
abstract = {Undefined strain starters are used for the production of many traditional and artisanal cheeses. Composition of undefined starters depends on several factors, and the diversity in strains and species significantly affects cheese quality and features. Culture-dependent approaches have long been used for the microbial profiling and functionalities of undefined cultures but underestimate their diversity due to culturability biases. Recently, culture-independent methods, based on high-throughput sequencing (HTS), have been preferred, with a significant boost in resolution power and sensitivity level. Amplicon targeted (AT) metagenomics, based on 16S rRNA sequencing, returned a larger microbiota diversity at genus and, sometimes, at species levels for artisanal starters of several PDO cheeses, but was inappropriate for populations with high strain diversity, and other gene targets were tested in AT approaches. Shotgun metagenomics (total DNA) and metatranscriptomics (total RNA), although are more powerful in depicting diversity and functionality of undefined cultures, have been rarely applied because of some limitations (e.g., high costs and laboriousness, need for bioinformatics skills). The advantages of HTS technologies are undoubted, but some hurdles need to be still overcame (e.g., resolution power, discrepancy between active and inactive cells, robust analytic pipelines, cost and time reduction for integrated approaches) so that HTS become routinary and convenient for defining complexity, microbial interactions (including host-phage relationships) and evolution in cheeses of undefined starters.},
}
@article {pmid33172994,
year = {2020},
author = {Hevroni, G and Flores-Uribe, J and Béjà, O and Philosof, A},
title = {Seasonal and diel patterns of abundance and activity of viruses in the Red Sea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {47},
pages = {29738-29747},
pmid = {33172994},
issn = {1091-6490},
mesh = {Aquatic Organisms/genetics/*virology ; DNA, Viral/isolation &amp; purification ; Indian Ocean ; Metagenome ; Microbial Interactions/genetics ; *Seasons ; Seawater/*microbiology ; Virome/*genetics ; Viruses/classification/*genetics/isolation &amp; purification ; },
abstract = {Virus-microbe interactions have been studied in great molecular details for many years in cultured model systems, yielding a plethora of knowledge on how viruses use and manipulate host machinery. Since the advent of molecular techniques and high-throughput sequencing, methods such as cooccurrence, nucleotide composition, and other statistical frameworks have been widely used to infer virus-microbe interactions, overcoming the limitations of culturing methods. However, their accuracy and relevance is still debatable as cooccurrence does not necessarily mean interaction. Here we introduce an ecological perspective of marine viral communities and potential interaction with their hosts, using analyses that make no prior assumptions on specific virus-host pairs. By size fractionating water samples into free viruses and microbes (i.e., also viruses inside or attached to their hosts) and looking at how viral group abundance changes over time along both fractions, we show that the viral community is undergoing a change in rank abundance across seasons, suggesting a seasonal succession of viruses in the Red Sea. We use abundance patterns in the different size fractions to classify viral clusters, indicating potential diverse interactions with their hosts and potential differences in life history traits between major viral groups. Finally, we show hourly resolved variations of intracellular abundance of similar viral groups, which might indicate differences in their infection cycles or metabolic capacities.},
}
@article {pmid32168762,
year = {2020},
author = {Shu, L and Ludwig, A and Peng, Z},
title = {Standards for Methods Utilizing Environmental DNA for Detection of Fish Species.},
journal = {Genes},
volume = {11},
number = {3},
pages = {},
pmid = {32168762},
issn = {2073-4425},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods/standards ; Environmental DNA/chemistry/*genetics ; Fishes/classification/*genetics ; Metagenomics/*methods/standards ; Reference Standards ; },
abstract = {Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.},
}
@article {pmid31975171,
year = {2020},
author = {Mattila, TM and Laenen, B and Slotte, T},
title = {Population Genomics of Transitions to Selfing in Brassicaceae Model Systems.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2090},
number = {},
pages = {269-287},
doi = {10.1007/978-1-0716-0199-0_11},
pmid = {31975171},
issn = {1940-6029},
mesh = {Brassicaceae/genetics/*physiology ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Genome, Plant ; Inbreeding ; Metagenomics/*methods ; Recombination, Genetic ; *Self-Fertilization ; *Self-Incompatibility in Flowering Plants ; },
abstract = {Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems. The maintenance of such systems over long evolutionary timescales suggests that outcrossing is favorable over a broad range of conditions. Conversely, SI has repeatedly been lost, often in association with transitions to self-fertilization (selfing). This transition is favored when the short-term advantages of selfing outweigh the costs, primarily inbreeding depression. The transition to selfing is expected to have major effects on population genetic variation and adaptive potential, as well as on genome evolution. In the Brassicaceae, many studies on the population genetic, gene regulatory, and genomic effects of selfing have centered on the model plant Arabidopsis thaliana and the crucifer genus Capsella. The accumulation of population genomics datasets have allowed detailed investigation of where, when and how the transition to selfing occurred. Future studies will take advantage of the development of population genetics theory on the impact of selfing, especially regarding positive selection. Furthermore, investigation of systems including recent transitions to selfing, mixed mating populations and/or multiple independent replicates of the same transition will facilitate dissecting the effects of mating system variation from processes driven by demography.},
}
@article {pmid31927795,
year = {2020},
author = {Zemb, O and Achard, CS and Hamelin, J and De Almeida, ML and Gabinaud, B and Cauquil, L and Verschuren, LMG and Godon, JJ},
title = {Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike-in standard.},
journal = {MicrobiologyOpen},
volume = {9},
number = {3},
pages = {e977},
pmid = {31927795},
issn = {2045-8827},
mesh = {Base Sequence ; Biodiversity ; *DNA Barcoding, Taxonomic/methods ; Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/chemistry/*genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.},
}
@article {pmid31902141,
year = {2020},
author = {Yu, H and Xue, D and Wang, Y and Zheng, W and Zhang, G and Wang, ZL},
title = {Molecular ecological network analysis of the response of soil microbial communities to depth gradients in farmland soils.},
journal = {MicrobiologyOpen},
volume = {9},
number = {3},
pages = {e983},
pmid = {31902141},
issn = {2045-8827},
mesh = {Biodiversity ; Environment ; *Farms ; Geography ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Soil Microbiology ; },
abstract = {Soil microorganisms are considered to be important indicators of soil fertility and soil quality. Most previous studies have focused solely on surface soil, but there were numerous active cells in deeper soil layers. However, studies regarding microbial communities in deeper soil layers were not comprehensive and sufficient. In this study, phylogenetic molecular ecological networks (pMENs) based on the 16S rRNA Miseq sequencing technique were applied to study the response of soil microbial communities to depth gradients and the changes of key genera along 3 meter depth gradients (0-0.2 m, 0.2-0.4 m 0.4-0.6 m, 0.6-0.8 m, 0.8-1.0 m, 1.0-1.3 m, 1.3-1.6 m, 1.6-2.0 m, 2.0-2.5 m, and 2.5-3.0 m). The results showed that the modularity of microbial communities was consistently high in all soil layers and each layer was similar, which indicated that microbial communities were more resistant to depth changes. The pMENs further demonstrated that microbial community interactions were stable as the depth increased and they cooperated well to adapt to changes in different soil gradients. This was evidenced by similar positive links, average degree, and average clustering coefficient. In addition, key genera were obtained by analyzing module hubs in the pMENs. There may be at least one dominant genus in each layer that adapted to and resisted changes in the soil environment. It seems microbial communities demonstrate a stable and strong adaptability to depth gradients in farmland soils.},
}
@article {pmid31893578,
year = {2020},
author = {Zhou, J and Yu, L and Zhang, J and Zhang, X and Xue, Y and Liu, J and Zou, X},
title = {Characterization of the core microbiome in tobacco leaves during aging.},
journal = {MicrobiologyOpen},
volume = {9},
number = {3},
pages = {e984},
pmid = {31893578},
issn = {2045-8827},
mesh = {*Aging ; Bacteria/classification/genetics ; Biodiversity ; Environment ; Humans ; Metagenomics/methods ; Microbiota/genetics ; Plant Leaves/*microbiology ; Tobacco/growth &amp; development/*microbiology ; },
abstract = {Microbiome plays an important role during the tobacco aging process which was an indispensable link in the production and processing of cigarettes. However, the structure and functions of microbiome have not been clarified during the tobacco aging process. In this study, 16S rDNA and ITS amplicon sequencing techniques were used to analyze the core microbiome of 15 tobacco samples from five different aging stages. The whole bacterial microbiome was classified into 29 microbial phyla and 132 orders. Enterobacteriales (63%), Pseudomonadales (16%), Sphingomonadales (8%), Xanthomonadales (4%), Burkholderiales (4%), Rhizobiales (3%), and Bacillales (2%) comprised the core bacterial microbiome. The whole fungal microbiome was classified into five microbial phyla and 52 orders. Incertae_sedis_Eurotiomycetes (27%), Wallemiales (25%), Sporidiobolales (17%), Capnodiales (5%), Eurotiales (2%), an unclassified Ascomycota (12%), and an unidentified Eurotiomycetes (4%) comprised the core fungal microbiome. FAPROTAX function prediction suggested that the core microbiome has a substantial potential for the carbon cycle, nitrate metabolism, aromatic compound degradation, chitinolysis, cellulolysis, and xylanolysis, but simultaneously, the core microbiome is also a source of human pathogens. The dynamics of the bacterial community were primarily determined by the total nitrogen in tobacco leaves during the aging process, while those of the fungal microbiome were primarily determined by total organic carbon. This study indicated that the core microbiome activities may play an important role in regulating the loss of carbon organic compounds and enhancing the secondary metabolites during tobacco leaves aging process.},
}
@article {pmid31880067,
year = {2020},
author = {Chen, T and Li, Y and Liang, J and Li, Y and Huang, Z},
title = {Gut microbiota of provisioned and wild rhesus macaques (Macaca mulatta) living in a limestone forest in southwest Guangxi, China.},
journal = {MicrobiologyOpen},
volume = {9},
number = {3},
pages = {e981},
pmid = {31880067},
issn = {2045-8827},
mesh = {Animal Feed ; Animals ; Biodiversity ; *Calcium Carbonate ; China ; *Forests ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; *Macaca mulatta ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The gut microbiota plays an important role in animal health and is strongly affected by the environment. Captivity and human source food have been shown to influence drastically the gut microbiota composition and function of wild animals. Therefore, in the present study, the gut microbiota of provisioned and wild populations of limestone-living rhesus macaques (Macaca mulatta) were compared using high-throughput 16S rRNA sequencing and bioinformatic analyses. The results indicated that provisioned macaques had a higher microbial richness than wild macaques, but there was no significant difference in the evenness of the gut microbiota between the two populations. Provisioned macaques also showed a higher abundance of Firmicutes and a lower abundance of Bacteroidetes than wild macaques. Functional analysis revealed that wild macaques had enriched microbial pathways involved in glycan biosynthesis and metabolism, transport and catabolism, and the digestive and endocrine systems, while provisioned macaques were richer in pathways associated with signaling molecules and interaction, neurodegenerative diseases. These differences were likely due to modification of the gut microbiota of the provisioned macaques to enable the digestion of new foods.},
}
@article {pmid31808296,
year = {2020},
author = {Zhang, Q and Geng, Z and Li, D and Ding, Z},
title = {Characterization and discrimination of microbial community and co-occurrence patterns in fresh and strong flavor style flue-cured tobacco leaves.},
journal = {MicrobiologyOpen},
volume = {9},
number = {2},
pages = {e965},
pmid = {31808296},
issn = {2045-8827},
mesh = {Biodiversity ; Eukaryotic Cells/classification ; *Fermentation ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; *Microbiota ; Neural Networks, Computer ; Phylogeny ; Plant Leaves/*microbiology ; Prokaryotic Cells/classification ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; *Tobacco ; },
abstract = {Fermentation, also known as aging, is vital for enhancing the quality of flue-cured tobacco leaves (FTLs). Aged FTLs demonstrate high-quality sensory characteristics, while unaged FTLs do not. Microbes play important roles in the FTL fermentation process. However, the eukaryotic microbial community diversity is poorly understood, as are microbial associations within FTLs. We aimed to characterize and compare the microbiota associated with two important categories, fresh and strong flavor style FTLs, and to reveal correlations between the microbial taxa within them. Based on 16S and 18S rRNA Illumina MiSeq sequencing, the community richness and diversity of prokaryotes were almost as high as that of eukaryotes. The dominant microbes of FTLs belonged to seven genera, including Pseudomonas, Bacillus, Methylobacterium, Acinetobacter, Sphingomonas, Neophaeosphaeria, and Cladosporium, of the Proteobacteria, Firmicutes, and Ascomycota phyla. According to partial least square discriminant analysis (PLS-DA), Xanthomonas, Franconibacter, Massilia, Quadrisphaera, Staphylococcus, Cladosporium, Lodderomyces, Symmetrospora, Golovinomyces, and Dioszegia were significantly positively correlated with fresh flavor style FTLs, while Xenophilus, Fusarium, unclassified Ustilaginaceae, Tilletiopsis, Cryphonectria, Colletotrichum, and Cyanodermella were significantly positively correlated with strong flavor style FTLs. Network analysis identified seven hubs, Aureimonas, Kocuria, Massilia, Brachybacterium, Clostridium, Dietzia, and Vishniacozyma, that may play important roles in FTL ecosystem stability, which may be destroyed by Myrmecridium. FTL microbiota was found to be correlated with flavor style. Species present in lower numbers than the dominant microbes might be used as microbial markers to discriminate different flavor style samples and to stabilize FTL microbial communities. This research advances our understanding of FTL microbiota and describes a means of discriminating between fresh and strong flavor FTLs based on their respective stable microbiota.},
}
@article {pmid31701637,
year = {2020},
author = {Ren, Q and Si, H and Yan, X and Liu, C and Ding, L and Long, R and Li, Z and Qiu, Q},
title = {Bacterial communities in the solid, liquid, dorsal, and ventral epithelium fractions of yak (Bos grunniens) rumen.},
journal = {MicrobiologyOpen},
volume = {9},
number = {2},
pages = {e963},
pmid = {31701637},
issn = {2045-8827},
mesh = {Animals ; Biodiversity ; Cattle ; Computational Biology/methods ; Gastric Mucosa/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rumen/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Yak (Bos grunniens) is an important and dominant livestock species in the challenging environment of the Qinghai-Tibetan Plateau. Rumen microbiota of the solid, liquid, and epithelium fractions play key roles in nutrient metabolism and contribute to host adaptation in ruminants. However, there is a little knowledge of the microbiota in these rumen fractions of yak. Therefore, we collected samples of solid, liquid, dorsal, and ventral epithelium fractions from five female yaks, then amplified bacterial 16S rRNA gene V4 regions and sequenced them using an Illumina MiSeq platform. Principal coordinates analysis detected significant differences in bacterial communities between the liquid, solid, and epithelium fractions, and between dorsal and ventral epithelium fractions. Rikenellaceae RC9, the families Lachnospiraceae and Ruminococcaceae, and Fibrobacter spp. were the abundant and enriched bacteria in solid fraction, while the genera Prevotella and Prevotellaceae UCG 003 were higher in the liquid fraction. Campylobacter spp., Comamonas spp., Desulfovibrio spp., and Solobacterium spp. were significantly higher in dorsal epithelium, while Howardella spp., Prevotellaceae UCG 001, Ruminococcaceae UCG 005, and Treponema 2 were enriched in the ventral epithelium. Comparison of predictive functional profiles among the solid, liquid, and dorsal, and ventral epithelium fractions also revealed significant differences. Microbiota in the ventral fraction of yak rumen also significantly differ from reported microbiota of cattle. In conclusion, our results improve our knowledge of the taxonomic composition and roles of yak rumen microbiota.},
}
@article {pmid31670480,
year = {2020},
author = {Quigley, KM and Alvarez Roa, C and Torda, G and Bourne, DG and Willis, BL},
title = {Co-dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles.},
journal = {MicrobiologyOpen},
volume = {9},
number = {2},
pages = {e959},
pmid = {31670480},
issn = {2045-8827},
mesh = {Age Factors ; Animals ; Anthozoa/*microbiology ; *Bacterial Physiological Phenomena ; Computational Biology/methods ; DNA, Ribosomal Spacer ; Gene Ontology ; Metagenomics/methods ; *Microbiota ; Molecular Typing ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; },
abstract = {Interactions between corals and their associated microbial communities (Symbiodiniaceae and prokaryotes) are key to understanding corals' potential for and rate of acclimatory and adaptive responses. However, the establishment of microalgal and bacterial communities is poorly understood during coral ontogeny in the wild. We examined the establishment and co-occurrence between multiple microbial communities using 16S rRNA (bacterial) and ITS2 rDNA (Symbiodiniaceae) gene amplicon sequencing in juveniles of the common coral, Acropora tenuis, across the first year of development. Symbiodiniaceae communities in juveniles were dominated by Durusdinium trenchii and glynnii (D1 and D1a), with lower abundances of Cladocopium (C1, C1d, C50, and Cspc). Bacterial communities were more diverse and dominated by taxa within Proteobacteria, Cyanobacteria, and Planctomycetes. Both communities were characterized by significant changes in relative abundance and diversity of taxa throughout the year. D1, D1a, and C1 were significantly correlated with multiple bacterial taxa, including Alpha-, Deltra-, and Gammaproteobacteria, Planctomycetacia, Oxyphotobacteria, Phycisphaerae, and Rhizobiales. Specifically, D1a tended to associate with Oxyphotobacteria and D1 with Alphaproteobacteria, although these associations may represent correlational and not causal relationships. Bioenergetic modeling combined with physiological measurements of coral juveniles (surface area and Symbiodiniaceae cell densities) identified key periods of carbon limitation and nitrogen assimilation, potentially coinciding with shifts in microbial community composition. These results demonstrate that Symbiodiniaceae and bacterial communities are dynamic throughout the first year of ontology and may vary in tandem, with important fitness effects on host juveniles.},
}
@article {pmid33453699,
year = {2021},
author = {Zheng, B and Liu, W and Xu, H and Li, J and Jiang, X},
title = {Occurrence and distribution of antimicrobial resistance genes in the soil of an industrial park in China: A metagenomics survey.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {273},
number = {},
pages = {116467},
doi = {10.1016/j.envpol.2021.116467},
pmid = {33453699},
issn = {1873-6424},
abstract = {As zoned areas of industries, industrial parks have great impacts on the environment. Several studies have demonstrated that chemical compounds and heavy metals released from industrial parks can contaminate soil, water, and air. However, as an emerging pollutant, antimicrobial resistance genes (ARGs) in industrial parks have not yet been investigated. Here, we collected soil samples from 35 sites in an industrial park in China and applied a metagenomics strategy to profile the ARGs and virulence factors (VFs). We further compared the relative abundance of ARGs between the sites (TZ_31-35) located in a beta-lactam antimicrobial-producing factory and other sites (TZ_1-30) in this industrial park. Metagenomic sequencing and assembly generated 14, 383, 065 contigs and 17, 631, 051 open reading frames (ORFs). Taxonomy annotation revealed Proteobacteria and Actinobacteria as the most abundant phylum and class, respectively. The 32 pathogenic bacterial genera listed in the virulence factor database (VFDB) were all identified from the soil metagenomes in this industrial park. In total, 685,354 ARGs (3.89% of the ORFs) and 272,694 virulence factors (VFs) (1.55% of the ORFs) were annotated. These ARGs exhibited resistance to several critically important antimicrobials, such as rifampins, fluroquinolones, and beta-lactams. In addition, no significant difference in the relative abundance of ARGs was observed between sites TZ_31-35 and TZ_1-30, indicating that ARGs have already disseminated widely in this industrial park. The present study gave us a better understanding of the whole picture of the resistome and virulome in the soil of the industrial park and suggested that we should treat the industrial park as a whole in the surveillance and maintenance of ARGs.},
}
@article {pmid33453487,
year = {2021},
author = {Cheng, X and Xu, J and Smith, G and Zhang, Y},
title = {Metagenomic insights into dissemination of antibiotic resistance across bacterial genera in wastewater treatment.},
journal = {Chemosphere},
volume = {271},
number = {},
pages = {129563},
doi = {10.1016/j.chemosphere.2021.129563},
pmid = {33453487},
issn = {1879-1298},
abstract = {The aim of this study was to evaluate the impacts of conventional wastewater treatment processes including secondary treatment and chlorination on the removal of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB), and to assess the association of ARGs with their potential hosts in each treatment process. The results showed chlorination with subinhibitory concentration (<8 mg/L) resulted in an increased ARB number in the disinfection effluent. qPCR analysis indicated secondary treatment increased relative abundance of ARGs in remaining bacteria whereas disinfection reduced the relative abundance of those genes effectively. Metagenomic analysis revealed a significant shift of dominating bacterial genera harboring ARGs. Along the treatment train, 48, 95 and 80 genera were identified to be the ARG carriers in primary effluent, secondary effluent, and disinfection effluent, respectively. It was also found that secondary treatment increased the diversity of potential ARG hosts while both secondary treatment and chlorination broadened the host range of some ARGs at the genus level, which may be attributed to the spread of antibiotic resistance across bacterial genera through horizontal transfer. This study highlights the growing concerns that wastewater treatment plants (WWTPs) may disseminate ARGs by associating this effect to specific treatment stages and by correlating ARGs with their bacterial hosts.},
}
@article {pmid33453422,
year = {2021},
author = {Tao, S and Wang, Z and Quan, C and Ge, Y and Qian, Q},
title = {The effects of ALA-PDT on microbiota in pilosebaceous units of patients with severe acne: A metagenomic study.},
journal = {Photodiagnosis and photodynamic therapy},
volume = {},
number = {},
pages = {102050},
doi = {10.1016/j.pdpdt.2020.102050},
pmid = {33453422},
issn = {1873-1597},
abstract = {BACKGROUND: 5-aminolevulinic acid mediated photodynamic therapy (ALA-PDT) is increasingly used to control severe acne. However, its impact on skin microbiota remains uncertain.<br><br>OBJECTIVES: We aimed to compare the makeup, diversity, and function of the microbiota in pilosebaceous units of patients with severe acne before and after ALA-PDT.<br><br>METHODS: A longitudinal cohort study was performed on 11 participants with severe facial acne. All patients were given 5%ALA-PDT every two weeks for three sessions in total. The contents of lesions were sampled for metagenomic sequencing at baseline and two weeks after of the first ALA-PDT.<br><br>RESULTS: Cutibacterium acnes was the most dominant species followed by Staphylococcus epidermidis and Pseudomonas fluorescens. Treatment with ALA-PDT led to clinical improvements in acne severity concurrent with a significant reduction in the relative abundance of C. acnes, while P. fluorescens increased significantly after ALA-PDT. No significant change was identified in other species. ALA-PDT administration was associated with an increased microbiota diversity and reductions in the relative abundance of the functional genes involved in energy metabolism and DNA replication.<br><br>CONCLUSIONS: ALA-PDT plays a therapeutic role by killingC. acnes, increasing P. fluorescens and the microbiome diversity, while inhibiting the function of microbiota in pilosebaceous units of severe acne.},
}
@article {pmid33453280,
year = {2021},
author = {Nilewski, S and Varatnitskaya, M and Masuch, T and Kusnezowa, A and Gellert, M and Baumann, AF and Lupilov, N and Kusnezow, W and Koch, MH and Eisenacher, M and Berkmen, M and Lillig, CH and Leichert, LI},
title = {Functional metagenomics of the thioredoxin superfamily.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {100247},
doi = {10.1074/jbc.RA120.016350},
pmid = {33453280},
issn = {1083-351X},
abstract = {Environmental sequence data of microbial communities now makes up the majority of public genomic information. The assignment of a function to sequences from these metagenomic sources is challenging, because organisms associated with the data are often uncharacterized and not cultivable. To overcome these challenges, we created a rationally designed expression library of metagenomic proteins covering the sequence space of the thioredoxin superfamily. This library of 100 individual proteins represents more than 22'000 thioredoxins found in the Global Ocean Sampling dataset. We screened this library for the functional rescue of Escherichia coli mutants lacking the thioredoxin-type reductase (ΔtrxA), isomerase (ΔdsbC), or oxidase (ΔdsbA). We were able to assign functions to more than a quarter of our representative proteins. The in vivo function of a given representative could not be predicted by phylogenetic relation but did correlate with the predicted isoelectric surface potential of the protein. Selected proteins were then purified, and we determined their activity using a standard insulin reduction assay and measured their redox potential. An unexpected gel shift of protein E5 during the redox potential determination revealed a redox cycle distinct from that of typical thioredoxin-superfamily oxidoreductases. Instead of the intramolecular disulfide bond formation typical for thioredoxins, this protein forms an intermolecular disulfide between the attacking cysteines of two separate subunits during its catalytic cycle. Our functional metagenomic approach proved not only useful to assign in vivo functions to representatives of thousands of proteins, but also uncovered a novel reaction mechanism in a seemingly well-known protein superfamily.},
}
@article {pmid33452983,
year = {2021},
author = {Grigorova, EV and Belkova, NL and Nemchenko, UM and Klimenko, ES and Pogodina, AV and Romanitsa, AI and Novikova, EA and Rychkova, LV},
title = {Metasequencing of V3-V4 Variable Regions of 16S rRNA Gene in Opportunistic Microbiota and Gut Biocenosis in Obese Adolescents.},
journal = {Bulletin of experimental biology and medicine},
volume = {},
number = {},
pages = {},
pmid = {33452983},
issn = {1573-8221},
abstract = {Opportunistic microorganisms in the gut biocenosis were studied in adolescents with normal body weight and obesity (patients consulted at the Clinical Department of Research Center of Family Health and Human Reproduction Problems). The biological material was studied by standard bacteriological methods, representatives of Enterobacteriaceae family were also characterized using metagenomic sequencing of V3-V4 variable regions of 16S gene rRNA. Gut microbiota of obese adolescents was unbalanced and was characterized by low levels of bifido- and lactoflora representatives, a spectrum of E. coli associations, and high prevalence of opportunistic microorganisms and their associations. Representatives of Enterobacteriaceae family were most often found in the gut microbiota of obese adolescents.},
}
@article {pmid33452484,
year = {2021},
author = {Zhang, JW and Dong, HP and Hou, LJ and Liu, Y and Ou, YF and Zheng, YL and Han, P and Liang, X and Yin, GY and Wu, DM and Liu, M and Li, M},
title = {Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {33452484},
issn = {1751-7370},
abstract = {Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood-Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.},
}
@article {pmid33452346,
year = {2021},
author = {Strange, JES and Leekitcharoenphon, P and Møller, FD and Aarestrup, FM},
title = {Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1600},
pmid = {33452346},
issn = {2045-2322},
support = {NNF16OC0021856//Novo Nordisk Fonden/ ; },
abstract = {Bacteriophages, or phages, are ubiquitous bacterial and archaeal viruses with an estimated total global population of 1031. It is well-known that wherever there are bacteria, their phage counterparts will be found, aiding in shaping the bacterial population. The present study used metagenomic data from global influent sewage in 79 cities in 60 countries to identify phages associated with bacteria and to explore their potential role in antimicrobial resistance gene (ARG) dissemination. The reads were mapped to known databases for bacteriophages and their abundances determined and correlated to geographic origin and the countries socio-economic status, as well as the abundances of bacterial species and ARG. We found that some phages were not equally distributed on a global scale, but their distribution was rather dictated by region and the socioeconomic status of the specific countries. This study provides a preliminary insight into the global and regional distribution of phages and their potential impact on the transmission of ARGs between bacteria. Moreover, the findings may indicate that phages in sewage could have adopted a lytic lifestyle, meaning that most may not be associated with bacteria and instead may be widely distributed as free-living phages, which are known to persist longer in the environment than their hosts. In addition, a significant correlation between phages and ARGs was obtained, indicating that phages may play a role in ARG dissemination. However, further analyses are needed to establish the true relationship between phages and ARGs due to a low abundance of the phages identified.},
}
@article {pmid33452030,
year = {2021},
author = {Gromala, M and Neufeld, JD and McConkey, BJ},
title = {Monitoring microbial populations and antibiotic resistance gene enrichment associated with Arctic waste stabilization ponds.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02914-20},
pmid = {33452030},
issn = {1098-5336},
abstract = {Wastewater management in the Canadian Arctic is challenging due to climate extremes, small population sizes, and lack of conventional infrastructure for wastewater treatment. Although many Northern communities use waste stabilization ponds (WSPs) as their primary form of wastewater treatment, few studies have explored WSP microbial communities and assessed effluent impacts on receiving waters from a microbiological perspective. Here we used 16S rRNA gene and metagenome sequencing to characterize WSP and receiving water microbial communities for two time points bracketing the spring WSP thaw in Baker Lake (Nunavut) and compared these results to other Nunavut WSPs in Cambridge Bay and Kugluktuk. Most amplicon sequence variants (ASVs) recovered from these WSP samples belonged to the phylum Proteobacteria, with considerable variation between the three locations and only six ASVs shared among the WSPs at >0.2% relative abundance. Wastewater indicator ASVs for the Baker Lake WSP were identified and few indicator ASVs were detected in samples originating from other upstream or downstream sites. The metagenomic data revealed a strong enrichment of antibiotic resistance genes for WSP samples, relative to downstream and reference samples, especially for genes associated with macrolide resistance. Together our results provide a baseline characterization for WSP microbial communities, demonstrate how indicator ASVs can be used to monitor attenuation and dilution of effluent microorganisms, and reveal that WSPs can serve as hotspots for antibiotic resistance genes.Importance Given that the microbial communities of Arctic waste stabilization ponds (WSPs) are poorly studied to date, our characterization of multiple WSP systems and time points provides important baseline data that will assist with ongoing monitoring of effluent impacts on downstream aquatic ecosystems in the Arctic. This research also identifies indicator ASVs of WSPs that will be helpful for future monitoring for WSP effluent attenuation and demonstrates that WSP microbial communities are enriched in antibiotic resistance genes. Given operational and infrastructure changes anticipated for wastewater treatment systems in the Arctic, baseline data such as these are essential for further development of safe and effective wastewater treatment systems.},
}
@article {pmid33452029,
year = {2021},
author = {Nilsen, M and Lokmic, A and Angell, IL and Carlsen, KCL and Carlsen, KH and Haugen, G and Hedlin, G and Jonassen, CM and Marsland, BJ and Nordlund, B and Rehbinder, EM and Saunders, CM and Skjerven, HO and Snipen, L and Staff, AC and Söderhäll, C and Vettukattil, R and Rudi, K},
title = {Fecal Microbiota Nutrient Utilization Potential Suggests Mucins as Drivers for Initial Gut Colonization of Mother-Child Shared Bacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02201-20},
pmid = {33452029},
issn = {1098-5336},
abstract = {The nutritional drivers for mother-child sharing of bacteria, and corresponding longitudinal trajectory of the infant gut microbiota development are not yet completely settled. We therefore aimed to characterize the mother-child sharing and the inferred nutritional utilization potential for the gut microbiota from a large unselected cohort. We analyzed in depth gut microbiota in 100 mother-child pairs enrolled antenatally from the general population-based PreventADALL cohort. Fecal samples collected at gestational week 18 for mothers and at birth (meconium), 3, 6, and 12 months for infants were analyzed by reduced metagenome sequencing to determine metagenome size and taxonomic composition. The nutrient utilization potential was determined based on the Virtual Metabolic Human (VMH, www.vmh.life) database. The estimated median metagenome size was ∼150 million base-pairs (bp) for mothers and ∼20 million bp at birth for the children. Longitudinal analyses revealed mother-child sharing (P < 0.05, chi-square test) from birth up to 6 months for 3 prevalent Bacteroides species (prevalence > 25% for all age groups). In multivariate ANOVA, the mother-child shared Bacteroides were associated with vaginal delivery (1.7% explained variance, P = 0.0001). Both vaginal delivery and mother-child sharing were associated with host derived mucins as nutrient sources. The age-related increase in metagenome size corresponded to an increased diversity in nutrient utilization, with dietary polysaccharides as the main age-related factor. Our results support host derived mucins as potential selection means for mother-child sharing of initial colonizers, while the age-related increase in diversity being associated with dietary polysaccharides.IMPORTANCE The initial bacterial colonization of human infants is crucial for lifelong health. Understanding factors driving this colonization will therefore be of high importance. Here we have used a novel high taxonomic resolution approach to deduce the nutrient utilization potential of the infant gut microbiota in a large longitudinal mother-child cohort. We found mucins as potential selection means for the initial colonization of mother-child shared bacteria, while the transition to a more adult-like microbiota was associated with dietary polysaccharide utilization potential. This knowledge will be important for future understanding of the importance of diet in shaping the gut microbiota composition and development during infancy.},
}
@article {pmid33452027,
year = {2021},
author = {Meziti, A and Rodriguez-R, LM and Hatt, JK and Peña-Gonzalez, A and Levy, K and Konstantinidis, KT},
title = {How reliably do metagenome-assembled genomes (MAGs) represent natural populations? Insights from comparing MAGs against isolate genomes derived from the same fecal sample.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02593-20},
pmid = {33452027},
issn = {1098-5336},
abstract = {The recovery of metagenome-assembled genomes (MAGs) from metagenomic data has recently become a common task for microbial studies. The strengths and limitations of the underlying bioinformatics algorithms are well appreciated by now based on performance tests with mock datasets of known composition. However, these mock datasets do not capture the complexity and diversity often observed within natural populations, since their construction typically relies on only a single genome of a given organism. Further, it remains unclear if MAGs can recover population variable (e.g., shared by >10% but <90% of the members of the population) as efficiently as core genes (e.g., shared by >90% of the members). To address these issues, we compared the gene variability of pathogenic Escherichia coli isolates from eight diarrheal samples, for which the isolate was the causative agent, against their corresponding MAGs recovered from the companion metagenomic dataset. Our analysis revealed that MAGs with completeness estimates near 95% captured only 77% of the population core genes and 50% of the variable genes, on average. Further, about 5% of the genes of these MAG were conservatively identified as missing in the isolate and were of different (non-Enterobacteriaceae) taxonomic origin, suggesting errors at the genome binning step, even though contamination estimates based on commonly used pipelines were only 1.5%. Therefore, the quality of MAGs may oftentimes be worse than estimated, and we offer examples of how to recognize and improve such MAGs to sufficient quality by -for instance- employing only contigs longer than 1,000bp for binning.IMPORTANCE Metagenome assembly and recovery of metagenome-assembled genomes (MAGs) have recently become common tasks for microbiome studies across environmental and clinical settings. However, to what extent MAGs can capture the genes of the population they represent remains speculative. Current approaches to evaluate MAG quality are limited to the recovery and copy number of universal, housekeeping genes but these genes represent a small fraction of the total genome, leaving the majority of the genome essentially inaccessible. If MAG quality in reality is lower than these approaches would estimate, this could have dramatic consequences for all downstream analyses and interpretations. In this study, we evaluated this issue using a novel approach that employs comparisons of MAGs to isolate genomes derived from the same samples. Further, our samples originated from a diarrhea case-control study, and thus our results are relevant for recovering the virulence factors of pathogens from metagenomic datasets.},
}
@article {pmid33452024,
year = {2021},
author = {Zhu, HZ and Zhang, ZF and Zhou, N and Jiang, CY and Wang, BJ and Cai, L and Wang, HM and Liu, SJ},
title = {Intensive Bacterial Cultivation and Genome Assembly Reveal Previously Unknown Bacteria and Metabolic Potential in Karst Caves.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02440-20},
pmid = {33452024},
issn = {1098-5336},
abstract = {Karst caves are widely distributed subsurface systems, and the microbiomes therein are proposed to be the driving force for cave evolution and biogeochemical cycling. In past years, culture-independent studies on the microbiomes of cave systems have been conducted, yet intensive microbial cultivation is still needed to validate the sequence-derived hypothesis and to disclose the microbial functions in cave ecosystems. In this study, the microbiomes of two karst caves in Guizhou Province in southwest China were examined. A total of 3,562 bacterial strains were cultivated from rock, water, and sediment samples, and 329 species (including 14 newly described species) of 102 genera were found. We created a cave bacterial genome collection of 218 bacterial genomes from a karst cave microbiome through the extraction of 204 database-derived genomes and de novo sequencing of 14 new bacterial genomes. The cultivated genome collection obtained in this study and the metagenome data from previous studies were used to investigate the bacterial metabolism and potential involvement in the carbon, nitrogen, and sulfur biogeochemical cycles in the cave ecosystem. New N2-fixing Azospirillum and alkane-oxidizing Oleomonas species were documented in the karst cave microbiome. Two pcaIJ clusters of the β-ketoadipate pathway that were abundant in both the cultivated microbiomes and the metagenomic data were identified, and their representatives from the cultivated bacterial genomes were functionally demonstrated. This large-scale cultivation of a cave microbiome represents the most intensive collection of cave bacterial resources to date and provides valuable information and diverse microbial resources for future cave biogeochemical research.IMPORTANCE Karst caves are oligotrophic environments that are dark, humid, and have a relative stable annual temperature. The bacteria diversity and their metabolisms are crucial for understanding the biogeochemical cycling in cave ecosystems. We integrated large-scale bacterial cultivation with metagenomic data-mining to explore the composition and metabolisms of the microbiomes in two karst cave systems. Our results reveal the presence of a highly diversified cave bacterial community, and 14 new bacterial species were described and genome-sequenced. In this study, we obtained the most intensive collection of cultivated microbial resources from karst caves to date and predicted the various important routes for the biogeochemical cycling of elements in cave ecosystems.},
}
@article {pmid33451492,
year = {2019},
author = {Li, S and Tang, H and Ye, Y},
title = {A Meta-proteogenomic Approach to Peptide Identification Incorporating Assembly Uncertainty and Genomic Variation.},
journal = {Molecular &amp; cellular proteomics : MCP},
volume = {18},
number = {8S1},
pages = {S183-S192},
doi = {10.1074/mcp.TIR118.001233},
pmid = {33451492},
issn = {1535-9484},
abstract = {Matching metagenomic and/or metatranscriptomic data, currently often under-used, can be useful reference for metaproteomic tandem mass spectra (MS/MS) data analysis. Here we developed a software pipeline for identification of peptides and proteins from metaproteomic MS/MS data using proteins derived from matching metagenomic (and metatranscriptomic) data as the search database, based on two novel approaches Graph2Pro (published) and Var2Pep (new). Graph2Pro retains and uses uncertainties of metagenome assembly for reference-based MS/MS data analysis. Var2Pep considers the variations found in metagenomic/metatranscriptomic sequencing reads that are not retained in the assemblies (contigs). The new software pipeline provides one stop application of both tools, and it supports the use of metagenome assembly from commonly used assemblers including MegaHit and metaSPAdes. When tested on two collections of multi-omic microbiome data sets, our pipeline significantly improved the identification rate of the metaproteomic MS/MS spectra by about two folds, comparing to conventional contig- or read-based approaches (the Var2Pep alone identified 5.6% to 24.1% more unique peptides, depending on the data set). We also showed that identified variant peptides are important for functional profiling of microbiomes. All results suggested that it is important to take into consideration of the assembly uncertainties and genomic variants to facilitate metaproteomic MS/MS data interpretation.},
}
@article {pmid33451316,
year = {2021},
author = {Li, W and Zhang, Q and Xu, Y and Zhang, X and Huang, Q and Su, Z},
title = {Severe pneumonia in adults caused by Tropheryma whipplei and Candida sp. infection: a 2019 case series.},
journal = {BMC pulmonary medicine},
volume = {21},
number = {1},
pages = {29},
pmid = {33451316},
issn = {1471-2466},
abstract = {BACKGROUND: Whipple's disease is a chronic infectious disease caused by the Gram-positive bacterium Tropheryma whipplei (TW), which not only affects the gastrointestinal tract and causes malabsorption of nutrients, but several other systems, such as the cardiovascular system, central nervous system, the joints, and the vascular system, can also be simultaneously involved. The aim of this report was to be able to alert the clinician to severe pneumonia caused by TW combined with Candida sp.<br><br>CASE PRESENTATION: The case study was conducted on patients in September and November 2019. After routine examination and treatment, the results were not satisfactory. A bronchoalveolar lavage (BAL) using metagenomics next-generation sequencing was conducted on two adults who presented with fever, cough, and progressive dyspnea and who had no history of gastrointestinal symptoms, immunodeficiency diseases, or use of immunosuppressive agents. TW and Candida sp. were detected in in BAL.<br><br>CONCLUSIONS: This is a report of life-threatening pneumonia caused by TW combined with Candida sp. in a Chinese population.},
}
@article {pmid33450352,
year = {2021},
author = {Nasser, B and Saito, Y and Alarawi, M and Humam, AA and Mineta, K and Gojobori, T},
title = {Characterization of microbiologically influenced corrosion by comprehensive metagenomic analysis of an inland oil field.},
journal = {Gene},
volume = {},
number = {},
pages = {145425},
doi = {10.1016/j.gene.2021.145425},
pmid = {33450352},
issn = {1879-0038},
abstract = {Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the global energy industry because it causes substantial economic losses associated with frequent part replacement and can lead to potential damage to entire crude oil fields. Previous studies revealed that corrosion is mainly caused by microbial activities in a process currently termed microbiologically influenced corrosion (MIC) or biocorrosion. Identifying the bacteria responsible for biocorrosion is crucial for its suppression. In this study, we analyzed the microbial communities present at corrosion sites in oil plant pipelines using comparative metagenomic analysis along with bioinformatics and statistics. We analyzed the microbial communities in pipelines in an oil field in which groundwater is used as injection water. We collected samples from four different facilities in the oil field. Metagenomic analysis revealed that the microbial community structures greatly differed even among samples from the same facility. Treatments such as biocide administration and demineralization at each location in the pipeline may have independently affected the microbial community structure. The results indicated that microbial inspection throughout the pipeline network is essential to prevent biocorrosion at industrial plants. By identifying the bacterial species responsible for biocorrosion, this study provides bacterial indicators to detect and classify biocorrosion. Furthermore, these species may serve as biomarkers to detect biocorrosion at an early stage. Then, appropriate management such as treatment with suitable biocides can be performed immediately and appropriately. Thus, our study will serve as a platform for obtaining microbial information related to biocorrosion to enable the development of a practical approach to prevent its occurrence.},
}
@article {pmid33449963,
year = {2021},
author = {Souto, BM and de Araújo, ACB and Hamann, PRV and Bastos, AR and Cunha, IS and Peixoto, J and Kruger, RH and Noronha, EF and Quirino, BF},
title = {Functional screening of a Caatinga goat (Capra hircus) rumen metagenomic library reveals a novel GH3 β-xylosidase.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0245118},
doi = {10.1371/journal.pone.0245118},
pmid = {33449963},
issn = {1932-6203},
abstract = {Functional screening of metagenomic libraries is an effective approach for identification of novel enzymes. A Caatinga biome goat rumen metagenomic library was screened using esculin as a substrate, and a gene from an unknown bacterium encoding a novel GH3 enzyme, BGL11, was identified. None of the BGL11 closely related genes have been previously characterized. Recombinant BGL11 was obtained and kinetically characterized. Substrate specificity of the purified protein was assessed using seven synthetic aryl substrates. Activity towards nitrophenyl-β-D-glucopyranoside (pNPG), 4-nitrophenyl-β-D-xylopyranoside (pNPX) and 4-nitrophenyl-β-D-cellobioside (pNPC) suggested that BGL11 is a multifunctional enzyme with β-glucosidase, β-xylosidase, and cellobiohydrolase activities. However, further testing with five natural substrates revealed that, although BGL11 has multiple substrate specificity, it is most active towards xylobiose. Thus, in its native goat rumen environment, BGL11 most likely functions as an extracellular β-xylosidase acting on hemicellulose. Biochemical characterization of BGL11 showed an optimal pH of 5.6, and an optimal temperature of 50°C. Enzyme stability, an important parameter for industrial application, was also investigated. At 40°C purified BGL11 remained active for more than 15 hours without reduction in activity, and at 50°C, after 7 hours of incubation, BGL11 remained 60% active. The enzyme kinetic parameters of Km and Vmax using xylobiose were determined to be 3.88 mM and 38.53 μmol.min-1.mg-1, respectively, and the Kcat was 57.79 s-1. In contrast to BLG11, most β-xylosidases kinetically studied belong to the GH43 family and have been characterized only using synthetic substrates. In industry, β-xylosidases can be used for plant biomass deconstruction, and the released sugars can be fermented into valuable bio-products, ranging from the biofuel ethanol to the sugar substitute xylitol.},
}
@article {pmid33449116,
year = {2021},
author = {Santona, A and Mhmoud, NA and Siddig, EE and Deligios, M and Fiamma, M and Bakhiet, SM and Barac, A and Paglietti, B and Rubino, S and Fahal, AH},
title = {Metagenomics of black grains: new highlights in the understanding of eumycetoma.},
journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
volume = {},
number = {},
pages = {},
doi = {10.1093/trstmh/traa177},
pmid = {33449116},
issn = {1878-3503},
abstract = {BACKGROUND: Eumycetoma is a chronic subcutaneous granulomatous disease that is endemic in Sudan and other countries. It can be caused by eight different fungal orders. The gold standard diagnostic test is culture, however, culture-independent methods such as imaging, histopathological and molecular techniques can support diagnosis, especially in cases of negative cultures.<br><br>METHODS: The amplicon-based internal transcribed spacer 2 metagenomic technique was used to study black grains isolated from 14 tissue biopsies from patients with mycetoma. Furthermore, mycological culture and surgical biopsy histopathological examinations of grains were performed.<br><br>RESULTS: Madurella mycetomatis (n=5) and Falciformispora spp. (n=4) organisms were identified by culture and confirmed by metagenomics. Metagenomics recognised, at the species level, Falciformispora as Falciformispora tompkinsii (n=3) and Falciformispora senegalensis (n=1), while in culture-negative cases (n=5), Madurella mycetomatis (n=3), Falciformispora senegalensis (n=1) and Fusarium spp. (n=1) were identified. Interestingly, the metagenomics results showed a 'consortium' of different fungi in each sample, mainly Ascomycota phylum, including various species associated with eumycetoma. The microbial co-occurrence in eumycetoma showed the co-presence of Madurella with Trichoderma, Chaetomium, Malasseziales and Sordariales spp., while Falciformispora co-presented with Inocybe and Alternaria and was in mutual exclusion with Subramaniula, Aspergillus and Trichothecium.<br><br>CONCLUSION: Metagenomics provides new insights into the aetiology of eumycetoma in samples with negative culture and into the diversity and complexity of grains mycobiota, calling into question the accuracy of traditional culture for the identification of causative agents.},
}
@article {pmid33448236,
year = {2021},
author = {Sawyer, A and Free, T and Martin, J},
title = {Metagenomics: preventing future pandemics.},
journal = {BioTechniques},
volume = {70},
number = {1},
pages = {1-4},
doi = {10.2144/btn-2020-0166},
pmid = {33448236},
issn = {1940-9818},
abstract = {Metagenomic approaches have been key to successful tracing and outbreak management during the COVID-19 pandemic. How can we use this knowledge to better prepare, strategize and prevent future pandemics? [Formula: see text].},
}
@article {pmid33447735,
year = {2020},
author = {Popescu, CR and Tembo, B and Chifisi, R and Cavanagh, MMM and Lee, AH and Chiluzi, B and Ciccone, EJ and Tegha, G and Alonso-Prieto, E and Claydon, J and Dunsmuir, D and Irvine, M and Dumont, G and Ansermino, JM and Wiens, MO and Juliano, JJ and Kissoon, N and Mvalo, T and Lufesi, N and Chiume-Kayuni, M and Lavoie, PM},
title = {Whole blood genome-wide transcriptome profiling and metagenomics next-generation sequencing in young infants with suspected sepsis in low-and middle-income countries: A study protocol.},
journal = {Gates open research},
volume = {4},
number = {},
pages = {139},
doi = {10.12688/gatesopenres.13172.1},
pmid = {33447735},
issn = {2572-4754},
abstract = {Conducting collaborative and comprehensive epidemiological research on neonatal sepsis in low- and middle-income countries (LMICs) is challenging due to a lack of diagnostic tests. This prospective study protocol aims to obtain epidemiological data on bacterial sepsis in newborns and young infants at Kamuzu Central Hospital in Lilongwe, Malawi. The main goal is to determine if the use of whole blood transcriptome host immune response signatures can help in the identification of infants who have sepsis of bacterial causes. The protocol includes a detailed clinical assessment with vital sign measurements, strict aseptic blood culture protocol with state-of-the-art microbial analyses and RNA-sequencing and metagenomics evaluations of host responses and pathogens, respectively. We also discuss the directions of a brief analysis plan for RNA sequencing data. This study will provide robust epidemiological data for sepsis in neonates and young infants in a setting where sepsis confers an inordinate burden of disease.},
}
@article {pmid33446856,
year = {2021},
author = {Boeckaerts, D and Stock, M and Criel, B and Gerstmans, H and De Baets, B and Briers, Y},
title = {Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1467},
pmid = {33446856},
issn = {2045-2322},
support = {01N02416//Special Research Fund of Ghent University/ ; FWO17/PDO/067)//Fonds Wetenschappelijk Onderzoek/ ; 1S32217N//Fonds Wetenschappelijk Onderzoek/ ; 3S003719//Fonds Wetenschappelijk Onderzoek,Belgium/ ; },
abstract = {Nowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.},
}
@article {pmid33446604,
year = {2021},
author = {Sulaiman, I and Wu, BG and Li, Y and Tsay, JC and Sauthoff, M and Scott, AS and Ji, K and Koralov, SB and Weiden, M and Clemente, J and Jones, D and Huang, YJ and Stringer, KA and Zhang, L and Geber, A and Banakis, S and Tipton, L and Ghedin, E and Segal, LN},
title = {Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism.},
journal = {The European respiratory journal},
volume = {},
number = {},
pages = {},
doi = {10.1183/13993003.03434-2020},
pmid = {33446604},
issn = {1399-3003},
abstract = {RATIONALE: Microbiome studies of the lower airway based on bacterial 16S rRNA gene sequencing assess microbial community structure but can only infer functional characteristics. Microbial products, such as short chain fatty acids (SCFAs), in the lower airways have significant impact on the host's immune tone. Thus, functional approaches to the analyses of the microbiome are necessary.<br><br>METHODS: Here we used upper and lower airway samples from a research bronchoscopy smoker cohort. In addition, we validated our results in an experimental mouse model.<br><br>MEASUREMENTS: We extended our microbiota characterisation beyond 16S rRNA gene sequencing with the use of whole genome (WGS) and RNA metatranscriptome sequencing. Short chain fatty acids (SCFA) were also measured in lower airway samples and correlated with each of the sequencing datasets. In the mouse model, 16S rRNA gene and RNA metatranscriptome sequencing were performed.<br><br>MAIN RESULTS: Functional evaluations of the lower airway microbiota using inferred metagenome, WGS and metatranscriptome were dissimilar. Comparison with measured levels of SCFAs shows that the inferred metagenome from the 16S rRNA gene sequencing data was poorly correlated, while better correlations were noted when SCFAs levels were compared with WGS and metatranscriptome. Modelling lower airway aspiration with oral commensals in a mouse model showed that the metatranscriptome most efficiently captures transient active microbial metabolism, which was overestimated by 16S rRNA gene sequencing.<br><br>CONCLUSIONS: Functional characterisation of the lower airway microbiota through metatranscriptome identify metabolically active organisms capable of producing metabolites with immunomodulatory capacity such as SCFAs.},
}
@article {pmid33446598,
year = {2021},
author = {Martin, RM and Kausch, M and Yap, K and Wehr, JD and Boyer, GL and Wilhelm, SW},
title = {Metagenome-Assembled Genome Sequences of Raphidiopsis raciborskii and Planktothrix agardhii from a Cyanobacterial Bloom in Kissena Lake, New York, USA.},
journal = {Microbiology resource announcements},
volume = {10},
number = {2},
pages = {},
pmid = {33446598},
issn = {2576-098X},
abstract = {Raphidiopsis raciborskii and Planktothrix agardhii are filamentous, potentially toxin-producing cyanobacteria that form nuisance blooms in fresh waters. Here, we report high-quality metagenome-assembled genome sequences of R. raciborskii and P. agardhii collected from a bloom in Kissena Lake, New York.},
}
@article {pmid33446592,
year = {2021},
author = {Arif, S and Nacke, H and Hoppert, M},
title = {Metagenome-Assembled Genome Sequences of a Biofilm Derived from Marsberg Copper Mine.},
journal = {Microbiology resource announcements},
volume = {10},
number = {2},
pages = {},
pmid = {33446592},
issn = {2576-098X},
abstract = {We sequenced the metagenome of a biofilm collected near a leachate stream of the Marsberg copper mine (Germany) and reconstructed eight metagenome-assembled genomes. These genomes yield copper resistance through Cu(I) oxidation via multiple copper oxidases and extrusion through copper-exporting P-type ATPases.},
}
@article {pmid33444853,
year = {2020},
author = {Yang, Y and Herbold, CW and Jung, MY and Qin, W and Cai, M and Du, H and Lin, JG and Li, X and Li, M and Gu, JD},
title = {Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration.},
journal = {Water research},
volume = {191},
number = {},
pages = {116798},
doi = {10.1016/j.watres.2020.116798},
pmid = {33444853},
issn = {1879-2448},
abstract = {Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.},
}
@article {pmid33444751,
year = {2021},
author = {Zeng, Z and Wang, C and Liu, C and Wang, B and Meng, X and Chen, Y and Guo, S},
title = {Follow-up of a Rickettsia felis encephalitis: Some new insights in clinical and imaging features.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijid.2020.12.090},
pmid = {33444751},
issn = {1878-3511},
abstract = {Rickettsia felis infection is a cause of unspecified encephalitis. However, the incidence of it was underestimated due to the intracellular feature of the pathogen and insufficient understanding of its clinical picture. Here we report a case of Rickettsia felis infection in a 26-year-old female who manifested with only certain neurological symptoms. With the lack of specific systemic inflammatory symptoms, the diagnosis was initially misdiagnosed as brain glioma. However, brain tissue biopsy showed prominent peri-vascular inflammatory infiltration which indicated inflammatory diseases. The spinal fluid Metagenomic Next-Generation Sequencing (mNGS) was taken after ruling out other common infectious and autoimmune diseases. The results suggested Rickettsia felis infection which was also supported by Weil Felix reaction in the serum. After the diagnosis was corrected as Rickettsia felis encephalitis, the patient was successfully treated with doxycycline and had a good prognosis in one-year follow up.},
}
@article {pmid33444437,
year = {2020},
author = {Nicholls, SM and Aubrey, W and De Grave, K and Schietgat, L and Creevey, CJ and Clare, A},
title = {On the complexity of haplotyping a microbial community.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaa977},
pmid = {33444437},
issn = {1367-4811},
abstract = {MOTIVATION: Population-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in culturing many microbes from an environment, we can still study these communities by isolating and sequencing DNA directly from an environment (metagenomics). Recovering the genomic sequences of all isoforms of a given gene across all organisms in a metagenomic sample would aid evolutionary and ecological insights into microbial ecosystems with potential benefits for medicine and biotechnology. A significant obstacle to this goal arises from the lack of a computationally tractable solution that can recover these sequences from sequenced read fragments. This poses a problem analogous to reconstructing the two sequences that make up the genome of a diploid organism (i.e. haplotypes), but for an unknown number of individuals and haplotypes.<br><br>RESULTS: The problem of single individual haplotyping (SIH) was first formalised by Lancia et al. in 2001. Now, nearly two decades later, we discuss the complexity of &quot;haplotyping&quot; metagenomic samples, with a new formalisation of Lancia et al's data structure that allows us to effectively extend the single individual haplotype problem to microbial communities. This work describes and formalizes the problem of recovering genes (and other genomic subsequences) from all individuals within a complex community sample, which we term the metagenomic individual haplotyping (MIH) problem. We also provide software implementations for a pairwise single nucleotide variant (SNV) co-occurrence matrix and greedy graph traversal algorithm.<br><br>Our reference implementation of the described pairwise SNV matrix (Hansel) and greedy haplotype path traversal algorithm (Gretel) are open source, MIT licensed and freely available online at github.com/samstudio8/hansel and github.com/samstudio8/gretel, respectively.},
}
@article {pmid33444384,
year = {2021},
author = {Maguire, M and Kase, JA and Roberson, D and Muruvanda, T and Brown, EW and Allard, M and Musser, SM and González-Escalona, N},
title = {Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0245172},
doi = {10.1371/journal.pone.0245172},
pmid = {33444384},
issn = {1932-6203},
abstract = {Shiga toxin-producing Escherichia coli (STEC) contamination of agricultural water might be an important factor to recent foodborne illness and outbreaks involving leafy greens. Closed bacterial genomes from whole genome sequencing play an important role in source tracking. We aimed to determine the limits of detection and classification of STECs by qPCR and nanopore sequencing using 24 hour enriched irrigation water artificially contaminated with E. coli O157:H7 (EDL933). We determined the limit of STEC detection by qPCR to be 30 CFU/reaction, which is equivalent to 105 CFU/ml in the enrichment. By using Oxford Nanopore's EPI2ME WIMP workflow and de novo assembly with Flye followed by taxon classification with a k-mer analysis software (Kraken2), E. coli O157:H7 could be detected at 103 CFU/ml (68 reads) and a complete fragmented E. coli O157:H7 metagenome-assembled genome (MAG) was obtained at 105-108 CFU/ml. Using a custom script to extract the E. coli reads, a completely closed MAG was obtained at 107-108 CFU/ml and a complete, fragmented MAG was obtained at 105-106 CFU/ml. In silico virulence detection for E. coli MAGs for 105-108 CFU/ml showed that the virulotype was indistinguishable from the spiked E. coli O157:H7 strain. We further identified the bacterial species in the un-spiked enrichment, including antimicrobial resistance genes, which could have important implications to food safety. We propose this workflow provides proof of concept for faster detection and complete genomic characterization of STECs from a complex microbial sample compared to current reporting protocols and could be applied to determine the limit of detection and assembly of other foodborne bacterial pathogens.},
}
@article {pmid33443810,
year = {2021},
author = {Zhuang, S and Hong, H and Zhang, L and Luo, Y},
title = {Spoilage-related microbiota in fish and crustaceans during storage: Research progress and future trends.},
journal = {Comprehensive reviews in food science and food safety},
volume = {20},
number = {1},
pages = {252-288},
doi = {10.1111/1541-4337.12659},
pmid = {33443810},
issn = {1541-4337},
support = {2018YFD0901001//National Key R&amp;D Program of China/ ; CARS-45//Earmarked Fund for China Agriculture Research System/ ; },
abstract = {Fish and crustaceans are highly perishable due to microbial growth and metabolism. Recent studies found that the spoilage process of fish and crustaceans is highly related to their microbiota composition. Microbiota of fish and crustaceans changes dramatically during storage and can be influenced by many factors (e.g., aquaculture environment, handling process, storage temperature, and various quality control techniques). Among them, many quality control techniques have exhibited efficient effects on inhibiting spoilage bacteria, regulating microbiota composition, and retarding quality deterioration. In this article, we elucidate the relationship between microbiota composition and fish/crustacean spoilage, demonstrate influencing factors of fish/crustaceans microbiota, and review various quality control techniques (especially plant-derived preservatives) including their preservative effects on microbiota and quality of fish and crustaceans. Besides, present and future trends of various detective methods used in microbiota analysis are also compared in this review, so as to provide guides for future microbiota studies. To conclude, novel preservation techniques (especially plant-derived preservatives) and hurdle technologies are expected to achieve comprehensive inhibitory effects on spoilage bacteria. Efficient delivery systems are promising in improving the compatibility of plant-derived preservatives with fish/crustaceans and enhancing their preservative effects. Besides, spoilage mechanisms of fishery products that involve complex metabolisms and microbial interactions need to be further elucidated, by using omics technologies like metagenomics, metatranscriptomics, and metabolomics.},
}
@article {pmid33443727,
year = {2021},
author = {Taketani, NF and Taketani, RG and Leite, SGF and Melo, IS and de Lima-Rizzo, AC and Andreote, FD and da Cunha, CD},
title = {Application of extracellular polymers on soil communities exposed to oil and nickel contamination.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {33443727},
issn = {1678-4405},
abstract = {The petrochemical industry is responsible for many accidental releases of pollutants in soil such as hydrocarbons and toxic metals. This co-contamination is responsible for a delay in the degradation of the organic pollution. Many successful technologies to remove these metals apply extracellular polymeric substances (EPS). In this study, we tested the application of an EPS from a Paenibacillus sp. to aid the bioremediation of soils contaminated with crude oil and nickel. We conducted a microcosm experiment to soils containing combinations of oil, nickel, and EPS. The final concentration of oil was evaluated with an infrared spectrometer. Also, we sequenced the metagenomes of the samples in an ion torrent sequencer. The application of EPS did not aid the removal of hydrocarbons with or without the presence of nickel. However, it led to a smaller decrease in the diversity indexes. EPS decreased the abundance of Actinobacteria and increased that of Proteobacteria. The EPS also decreased the connectivity among Actinobacteria in the network analysis. The results indicated that the addition of EPS had a higher effect on the community structure than nickel. Altogether, our results indicate that this approach did not aid the bioremediation of hydrocarbons likely due to its effect in the community structure that affected hydrocarbonoclastic microorganisms.},
}
@article {pmid33443632,
year = {2021},
author = {Nkansah-Boadu, F and Hatam, I and Baldwin, SA},
title = {Microbial consortia capable of reducing selenate in the presence of nitrate enriched from coalmining-impacted environments.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {33443632},
issn = {1432-0614},
support = {UPP026//Genome British Columbia/ ; },
abstract = {Biological treatment to remove dissolved selenium from mine-impacted water is often inhibited by the co-contaminant nitrate. In this work, we enriched microbial consortia capable of removing dissolved selenium in the presence of nitrate from native bacteria at sites influenced by coalmine seepages with elevated concentrations of Se, nitrate, and sulfate. Enrichments were collected from sediments in different vegetated or non-vegetated seepage collection ponds, and all demonstrated the potential for dissolved selenium removal. Nitrate inhibited dissolved selenium removal rates in four of these enrichments. However, microorganisms enriched from a mine seepage influenced natural vegetated marsh removed dissolved Se and nitrate simultaneously. Additionally, enrichments from one seepage collection pond achieved enhanced dissolved selenium removal in the presence of nitrate. Based on functional metagenomics, the dominant species with the metabolic capacity for selenate reduction were classified in Orders Enterobacterales and Clostridiales. Most putative selenate reductases identified as either ygfK, associated with selenoprotein synthesis or production of methylated organoselenium compounds, and narG, nitrate reductases with an affinity also for selenate.Key points• Enriched mine influenced sediment bacteria have the capacity for removal of dissolved Se species.• Consortia from a vegetated natural marsh reduced Se without inhibition from nitrate.• Nitrate stimulated the removal of Se by consortia from a disused tailing pond.},
}
@article {pmid33441735,
year = {2021},
author = {Díaz-Nieto, LM and Gil, MF and Lazarte, JN and Perotti, MA and Berón, CM},
title = {Culex quinquefasciatus carrying Wolbachia is less susceptible to entomopathogenic bacteria.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1094},
pmid = {33441735},
issn = {2045-2322},
support = {ANPCyT PICT-2015-0575//Agencia Nacional de Promoción Científica y Tecnológica/ ; PUE 2017-0101//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; 15/E883 EXA925/19//Universidad Nacional de Mar del Plata/ ; },
abstract = {In an attempt to evaluate the susceptibility of the mosquito Culex quinquefasciatus to bacterial agents, a population naturally infected with a Wolbachia pipientis wPipSJ native strain was tested against the action of three bacterial mosquitocides, Bacillus thuringiensis subsp. israelensis, Bacillus wiedmannii biovar thuringiensis and Lysinibacillus sphaericus. Tests were carried out on mosquito larvae with and without Wolbachia (controls). Cx. quinquefasciatus naturally infected with the native wPipSJ strain proved to be more resistant to the pathogenic action of the three mosquitocidal bacterial strains. Additionally, wPipSJ was fully characterised using metagenome-assembled genomics, PCR-RFLP (PCR-Restriction Fragment Length Polymorphism) and MLST (MultiLocus Sequence Typing) analyses. This Wolbachia strain wPipSJ belongs to haplotype I, group wPip-III and supergroup B, clustering with other mosquito wPip strains, such as wPip PEL, wPip JHB, wPip Mol, and wAlbB; showing the southernmost distribution in America. The cytoplasmic incompatibility phenotype of this strain was revealed via crosses between wildtype (Wolbachia+) and antibiotic treated mosquito populations. The results of the tests with the bacterial agents suggest that Cx. quinquefasciatus naturally infected with wPipSJ is less susceptible to the pathogenic action of mosquitocidal bacterial strains when compared with the antibiotic-treated mosquito isoline, and is more susceptible to B. thuringiensis subsp. israelensis than to the other two mosquitocidal agents.},
}
@article {pmid33441409,
year = {2021},
author = {Fishbein, SRS and Hink, T and Reske, KA and Cass, C and Struttmann, E and Iqbal, ZH and Seiler, S and Kwon, JH and Burnham, CA and Dantas, G and Dubberke, ER},
title = {Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients.},
journal = {mSphere},
volume = {6},
number = {1},
pages = {},
pmid = {33441409},
issn = {2379-5042},
abstract = {Clostridioides difficile infection (CDI) is most commonly diagnosed using nucleic acid amplification tests (NAAT); the low positive predictive value of these assays results in patients colonized with C. difficile unnecessarily receiving CDI treatment antibiotics. The risks and benefits of antibiotic treatment in individuals with such cases are unknown. Fecal samples of NAAT-positive, toxin enzyme immunoassay (EIA)-negative patients were collected before, during, and after randomization to vancomycin (n = 8) or placebo (n = 7). C. difficile and antibiotic-resistant organisms (AROs) were selectively cultured from fecal and environmental samples. Shotgun metagenomics and comparative isolate genomics were used to understand the impact of oral vancomycin on the microbiome and environmental contamination. Overall, 80% of placebo patients and 71% of vancomycin patients were colonized with C. difficile posttreatment. One person randomized to placebo subsequently received treatment for CDI. In the vancomycin-treated group, beta-diversity (P = 0.0059) and macrolide-lincosamide-streptogramin (MLS) resistance genes (P = 0.037) increased after treatment; C. difficile and vancomycin-resistant enterococci (VRE) environmental contamination was found in 53% of patients and 26% of patients, respectively. We found that vancomycin alters the gut microbiota, does not permanently clear C. difficile, and is associated with VRE colonization/environmental contamination. (This study has been registered at ClinicalTrials.gov under registration no. NCT03388268.)IMPORTANCE A gold standard diagnostic for Clostridioides difficile infection (CDI) does not exist. An area of controversy is how to manage patients whose stool tests positive by nucleic acid amplification tests but negative by toxin enzyme immunoassay. Existing data suggest most of these patients do not have CDI, but most are treated with oral vancomycin. Potential benefits to treatment include a decreased risk for adverse outcomes if the patient does have CDI and the potential to decrease C. difficile shedding/transmission. However, oral vancomycin perturbs the intestinal microbiota and promotes antibiotic-resistant organism colonization/transmission. We conducted a double-blinded randomized controlled trial to assess the risk-benefit of oral vancomycin treatment in this population. Oral vancomycin did not result in long-term clearance of C. difficile, perturbed the microbiota, and was associated with colonization/shedding of vancomycin-resistant enterococci. This work underscores the need to better understand this population of patients in the context of C. difficile/ARO-related outcomes and transmission.},
}
@article {pmid33441133,
year = {2021},
author = {Lu, C and Zhang, Z and Cai, Z and Zhu, Z and Qiu, Y and Wu, A and Jiang, T and Zheng, H and Peng, Y},
title = {Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics.},
journal = {BMC biology},
volume = {19},
number = {1},
pages = {5},
pmid = {33441133},
issn = {1741-7007},
support = {2016YFD0500300//National Key Plan for Scientific Research and Development of China/ ; 2018JJ3039//Hunan Provincial Natural Science Foundation of China/ ; 2019JJ50035//Hunan Provincial Natural Science Foundation of China/ ; 2020JJ3006//Hunan Provincial Natural Science Foundation of China/ ; 31671371//National Natural Science Foundation of China/ ; 81902070//National Natural Science Foundation of China/ ; 2016-I2M-1-005//Chinese Academy of Medical Sciences/ ; },
abstract = {BACKGROUND: Viruses are ubiquitous biological entities, estimated to be the largest reservoirs of unexplored genetic diversity on Earth. Full functional characterization and annotation of newly discovered viruses requires tools to enable taxonomic assignment, the range of hosts, and biological properties of the virus. Here we focus on prokaryotic viruses, which include phages and archaeal viruses, and for which identifying the viral host is an essential step in characterizing the virus, as the virus relies on the host for survival. Currently, the method for determining the viral host is either to culture the virus, which is low-throughput, time-consuming, and expensive, or to computationally predict the viral hosts, which needs improvements at both accuracy and usability. Here we develop a Gaussian model to predict hosts for prokaryotic viruses with better performances than previous computational methods.<br><br>RESULTS: We present here Prokaryotic virus Host Predictor (PHP), a software tool using a Gaussian model, to predict hosts for prokaryotic viruses using the differences of k-mer frequencies between viral and host genomic sequences as features. PHP gave a host prediction accuracy of 34% (genus level) on the VirHostMatcher benchmark dataset and a host prediction accuracy of 35% (genus level) on a new dataset containing 671 viruses and 60,105 prokaryotic genomes. The prediction accuracy exceeded that of two alignment-free methods (VirHostMatcher and WIsH, 28-34%, genus level). PHP also outperformed these two alignment-free methods much (24-38% vs 18-20%, genus level) when predicting hosts for prokaryotic viruses which cannot be predicted by the BLAST-based or the CRISPR-spacer-based methods alone. Requiring a minimal score for making predictions (thresholding) and taking the consensus of the top 30 predictions further improved the host prediction accuracy of PHP.<br><br>CONCLUSIONS: The Prokaryotic virus Host Predictor software tool provides an intuitive and user-friendly API for the Gaussian model described herein. This work will facilitate the rapid identification of hosts for newly identified prokaryotic viruses in metagenomic studies.},
}
@article {pmid33440837,
year = {2021},
author = {Bredon, M and Depuydt, E and Brisson, L and Moulin, L and Charles, C and Haenn, S and Moumen, B and Bouchon, D},
title = {Effects of Dysbiosis and Dietary Manipulation on the Digestive Microbiota of a Detritivorous Arthropod.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/microorganisms9010148},
pmid = {33440837},
issn = {2076-2607},
support = {BiodivUP//State-Region Planning Contracts (CPER), European Regional Development Fund (FEDER)/ ; },
abstract = {The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host's diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the &quot;eco-holobiont&quot; conceptualization of macroorganisms.},
}
@article {pmid33440311,
year = {2020},
author = {Kant Bhatia, S and Vivek, N and Kumar, V and Chandel, N and Thakur, M and Kumar, D and Yang, YH and Pugazendhi, A and Kumar, G},
title = {Molecular biology interventions for activity improvement and production of industrial enzymes.},
journal = {Bioresource technology},
volume = {324},
number = {},
pages = {124596},
doi = {10.1016/j.biortech.2020.124596},
pmid = {33440311},
issn = {1873-2976},
abstract = {Metagenomics and directed evolution technology have brought a revolution in search of novel enzymes from extreme environment and improvement of existing enzymes and tuning them towards certain desired properties. Using advanced tools of molecular biology i.e. next generation sequencing, site directed mutagenesis, fusion protein, surface display, etc. now researchers can engineer enzymes for improved activity, stability, and substrate specificity to meet the industrial demand. Although many enzymatic processes have been developed up to industrial scale, still there is a need to overcome limitations of maintaining activity during the catalytic process. In this article recent developments in enzymes industrial applications and advancements in metabolic engineering approaches to improve enzymes efficacy and production are reviewed.},
}
@article {pmid33440055,
year = {2021},
author = {Luan, Y and Hu, H and Liu, C and Chen, B and Liu, X and Xu, Y and Luo, X and Chen, J and Ye, B and Huang, F and Wang, J and Duan, C},
title = {A Proof-of-concept study of an automated solution for clinical metagenomic Next-Generation Sequencing.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jam.15003},
pmid = {33440055},
issn = {1365-2672},
abstract = {AIMS: Metagenomic next-generation sequencing (mNGS) has been utilized for diagnosing infectious diseases. It is a culture-free and hypothesis-free nucleic acid test for diagnosing all pathogens with known genomic sequences, including bacteria, fungi, viruses, and parasites. While this technique greatly expands the clinical capacity of pathogen detection, it is a second-line choice due to lengthy procedures and microbial contaminations introduced from wet-lab processes. As a result, we aimed to reduce the hands-on time and exogenous contaminations in mNGS.<br><br>METHODS AND RESULTS: We developed a device (NGSmaster) that automates the wet-lab workflow, including nucleic acid extraction, PCR-free library preparation and purification. It shortens the sample-to-results time to 16 and 18.5 hours for DNA and RNA sequencing, respectively. We used it to test cultured bacteria for validation of the workflow and bioinformatic pipeline. We also compared PCR-free with PCR-based library prep and discovered no differences in microbial reads. Moreover, we analyzed results by automation and manual testing and found that automation can significantly reduce microbial contaminations. Finally, we tested artificial and clinical samples and showed mNGS results were concordant with traditional culture.<br><br>CONCLUSION: NGSmaster can fulfill the microbiological diagnostic needs in a variety of sample types.<br><br>This study opens up an opportunity of performing in-house mNGS to reduce turnaround time and workload, instead of transferring potentially contagious specimen to a third-party laboratory.},
}
@article {pmid33439104,
year = {2021},
author = {Manandhar, I and Alimadadi, A and Aryal, S and Munroe, PB and Joe, B and Cheng, X},
title = {Gut microbiome-based supervised machine learning for clinical diagnosis of inflammatory bowel diseases.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00360.2020},
pmid = {33439104},
issn = {1522-1547},
support = {Dean's Postdoctoral to Faculty Fellowship//University of Toledo College of Medicine and Life Sciences/ ; P30 Core Center Pilot Grant//NIDA Center of Excellence in Omics, Systems Genetics, and the Addictome/ ; HL143082//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; },
abstract = {Despite the availability of various diagnostic tests for inflammatory bowel diseases (IBD), misdiagnosis of IBD occurs frequently, and thus there is a clinical need to further improve the diagnosis of IBD. As gut dysbiosis is reported in IBD patients, we hypothesized that supervised machine learning (ML) could be used to analyze gut microbiome data for predictive diagnostics of IBD. To test our hypothesis, fecal 16S metagenomic data of 729 IBD and 700 non-IBD subjects from the American Gut Project were analyzed using five different ML algorithms. Fifty differential bacterial taxa were identified (LEfSe: LDA > 3) between the IBD and non-IBD groups, and ML classifications trained with these taxonomic features using random forest (RF) achieved a testing AUC of ~0.80. Next, we tested if operational taxonomic units (OTUs), instead of bacterial taxa, could be used as ML features for diagnostic classification of IBD. Top 500 high-variance OTUs were used for ML training and an improved testing AUC of ~0.82 (RF) was achieved. Lastly, we tested if supervised ML could be used for differentiating Crohn's disease (CD) and ulcerative colitis (UC). Using 331 CD and 141 UC samples, 117 differential bacterial taxa (LEfSe: LDA > 3) were identified, and the RF model trained with differential taxonomic features or high-variance OTU features achieved a testing AUC > 0.90. In summary, our study demonstrates the promising potential of artificial intelligence via supervised ML modeling for predictive diagnostics of IBD using gut microbiome data.},
}
@article {pmid33439103,
year = {2021},
author = {Cuna, AC and Morowitz, MJ and Ahmed, I and Umar, S and Sampath, V},
title = {Dynamics of the Preterm Gut Microbiome in Health and Disease.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00399.2020},
pmid = {33439103},
issn = {1522-1547},
support = {R01DK117296//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; K08DK125735//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
abstract = {Advances in metagenomics have allowed a detailed study of the gut microbiome, and its role in human health and disease. Infants born prematurely possess a fragile gut microbial ecosystem that is vulnerable to perturbation. Alterations in the developing gut microbiome in preterm infants are linked to life-threatening diseases such as necrotizing enterocolitis (NEC) and late onset sepsis; and may impact future risk of asthma, atopy, obesity, and psychosocial disease. In this mini review, we summarize recent literature on the origins and patterns of development of the preterm gut microbiome in the perinatal period. The host-microbiome-environmental factors that portend development of dysbiotic intestinal microbial patterns associated with NEC and sepsis are reviewed. Strategies to manipulate the microbiome and mitigate dysbiosis, including the use of probiotics and prebiotics will also be discussed. Finally, we explore the challenges and future directions of gut microbiome research in preterm infants.},
}
@article {pmid33438892,
year = {2021},
author = {Peters, BA and Xue, X and Wang, Z and Usyk, M and Santoro, N and Sharma, A and Anastos, K and Tien, PC and Golub, ET and Weber, KM and Gustafson, D and Kaplan, RC and Burk, R and Qi, Q},
title = {Menopausal status and observed differences in the gut microbiome in women with and without HIV infection.},
journal = {Menopause (New York, N.Y.)},
volume = {Publish Ahead of Print},
number = {},
pages = {},
doi = {10.1097/GME.0000000000001730},
pmid = {33438892},
issn = {1530-0374},
abstract = {OBJECTIVE: Gut microbiota respond to host physiological phenomena, yet little is known regarding shifts in the gut microbiome due to menopausal hormonal and metabolic changes in women. HIV infection impacts menopause and may also cause gut dysbiosis. We therefore sought to determine the association between menopausal status and gut microbiome composition in women with and without HIV.<br><br>METHODS: Gut microbiome composition was assessed in stool from 432 women (99 premenopausal HIV+, 71 premenopausal HIV-, 182 postmenopausal HIV+, 80 postmenopausal HIV-) via 16S rRNA gene sequencing. We examined cross-sectional associations of menopause with gut microbiota overall diversity and composition, and taxon and inferred metagenomic pathway abundance. Models were stratified by HIV serostatus and adjusted for age, HIV-related variables, and other potential confounders.<br><br>RESULTS: Menopause, ie post- versus premenopausal status, was associated with overall microbial composition only in women with HIV (permutational MANOVA of Jensen Shannon Divergence: P = 0.01). In women with HIV, menopause was associated with enrichment of gram-negative order Enterobacteriales, depletion of highly abundant taxa within Prevotella copri, and alterations in other low-abundance taxa. Additionally, menopause in women with HIV was associated with enrichment of metagenomic pathways related to Enterobacteriales, including degradation of amino acids and phenolic compounds, biosynthesis of enterobactin, and energy metabolism pathways. Menopause-related differences in some low-abundance taxa were also observed in women without HIV.<br><br>CONCLUSIONS: A changing gut microbiome may be an overlooked phenomenon of reproductive aging in women with HIV. Longitudinal assessments across all reproductive stages are necessary to confirm these findings and identify health implications.},
}
@article {pmid33438731,
year = {2021},
author = {Kautsar, SA and van der Hooft, JJJ and de Ridder, D and Medema, MH},
title = {BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters.},
journal = {GigaScience},
volume = {10},
number = {1},
pages = {},
doi = {10.1093/gigascience/giaa154},
pmid = {33438731},
issn = {2047-217X},
abstract = {BACKGROUND: Genome mining for biosynthetic gene clusters (BGCs) has become an integral part of natural product discovery. The >200,000 microbial genomes now publicly available hold information on abundant novel chemistry. One way to navigate this vast genomic diversity is through comparative analysis of homologous BGCs, which allows identification of cross-species patterns that can be matched to the presence of metabolites or biological activities. However, current tools are hindered by a bottleneck caused by the expensive network-based approach used to group these BGCs into gene cluster families (GCFs).<br><br>RESULTS: Here, we introduce BiG-SLiCE, a tool designed to cluster massive numbers of BGCs. By representing them in Euclidean space, BiG-SLiCE can group BGCs into GCFs in a non-pairwise, near-linear fashion. We used BiG-SLiCE to analyze 1,225,071 BGCs collected from 209,206 publicly available microbial genomes and metagenome-assembled genomes within 10 days on a typical 36-core CPU server. We demonstrate the utility of such analyses by reconstructing a global map of secondary metabolic diversity across taxonomy to identify uncharted biosynthetic potential. BiG-SLiCE also provides a &quot;query mode&quot; that can efficiently place newly sequenced BGCs into previously computed GCFs, plus a powerful output visualization engine that facilitates user-friendly data exploration.<br><br>CONCLUSIONS: BiG-SLiCE opens up new possibilities to accelerate natural product discovery and offers a first step towards constructing a global and searchable interconnected network of BGCs. As more genomes are sequenced from understudied taxa, more information can be mined to highlight their potentially novel chemistry. BiG-SLiCE is available via https://github.com/medema-group/bigslice.},
}
@article {pmid33437563,
year = {2021},
author = {Pabbathi, NPP and Velidandi, A and Tavarna, T and Gupta, S and Raj, RS and Gandam, PK and Baadhe, RR},
title = {Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review.},
journal = {Biomass conversion and biorefinery},
volume = {},
number = {},
pages = {1-28},
doi = {10.1007/s13399-020-01186-y},
pmid = {33437563},
issn = {2190-6815},
abstract = {As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.},
}
@article {pmid33436875,
year = {2021},
author = {Shukla, PK and Meena, AS and Dalal, K and Canelas, C and Samak, G and Pierre, JF and Rao, R},
title = {Chronic stress and corticosterone exacerbate alcohol-induced tissue injury in the gut-liver-brain axis.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {826},
pmid = {33436875},
issn = {2045-2322},
support = {I01BX003014//U.S. Department of Veterans Affairs/ ; R01AA12307/NH/NIH HHS/United States ; },
abstract = {Alcohol use disorders are associated with altered stress responses, but the impact of stress or stress hormones on alcohol-associated tissue injury remain unknown. We evaluated the effects of chronic restraint stress on alcohol-induced gut barrier dysfunction and liver damage in mice. To determine whether corticosterone is the stress hormone associated with the stress-induced effects, we evaluated the effect of chronic corticosterone treatment on alcoholic tissue injury at the Gut-Liver-Brain (GLB) axis. Chronic restraint stress synergized alcohol-induced epithelial tight junction disruption and mucosal barrier dysfunction in the mouse intestine. These effects of stress on the gut were reproduced by corticosterone treatment. Corticosterone synergized alcohol-induced expression of inflammatory cytokines and chemokines in the colonic mucosa, and it potentiated the alcohol-induced endotoxemia and systemic inflammation. Corticosterone also potentiated alcohol-induced liver damage and neuroinflammation. Metagenomic analyses of 16S RNA from fecal samples indicated that corticosterone modulates alcohol-induced changes in the diversity and abundance of gut microbiota. In Caco-2 cell monolayers, corticosterone dose-dependently potentiated ethanol and acetaldehyde-induced tight junction disruption and barrier dysfunction. These data indicate that chronic stress and corticosterone exacerbate alcohol-induced mucosal barrier dysfunction, endotoxemia, and systemic alcohol responses. Corticosterone-mediated promotion of alcohol-induced intestinal epithelial barrier dysfunction and modulation of gut microbiota may play a crucial role in the mechanism of stress-induced promotion of alcohol-associated tissue injury at the GLB axis.},
}
@article {pmid33436515,
year = {2021},
author = {Tláskal, V and Brabcová, V and Větrovský, T and Jomura, M and López-Mondéjar, R and Oliveira Monteiro, LM and Saraiva, JP and Human, ZR and Cajthaml, T and Nunes da Rocha, U and Baldrian, P},
title = {Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33436515},
issn = {2379-5077},
abstract = {Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO2 emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO2 efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils.IMPORTANCE Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles.},
}
@article {pmid33436509,
year = {2021},
author = {Meier, DV and Imminger, S and Gillor, O and Woebken, D},
title = {Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33436509},
issn = {2379-5077},
abstract = {Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.},
}
@article {pmid33436440,
year = {2021},
author = {Griesenauer, B and González-Beiras, C and Fortney, KR and Lin, H and Gao, X and Godornes, C and Nelson, DE and Katz, BP and Lukehart, SA and Mitjà, O and Dong, Q and Spinola, SM},
title = {Streptococcus pyogenes Is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island.},
journal = {mBio},
volume = {12},
number = {1},
pages = {},
pmid = {33436440},
issn = {2150-7511},
abstract = {Exudative cutaneous ulcers (CU) in yaws-endemic areas are associated with Treponema pallidum subsp. pertenue (TP) and Haemophilus ducreyi (HD), but one-third of CU cases are idiopathic (IU). Using mass drug administration (MDA) of azithromycin, a yaws eradication campaign on Lihir Island in Papua New Guinea reduced but failed to eradicate yaws; IU rates remained constant throughout the campaign. To identify potential etiologies of IU, we obtained swabs of CU lesions (n = 279) and of the skin of asymptomatic controls (AC; n = 233) from the Lihir Island cohort and characterized their microbiomes using a metagenomics approach. CU bacterial communities were less diverse than those of the AC. Using real-time multiplex PCR with pathogen-specific primers, we separated CU specimens into HD-positive (HD+), TP+, HD+TP+, and IU groups. Each CU subgroup formed a distinct bacterial community, defined by the species detected and/or the relative abundances of species within each group. Streptococcus pyogenes was the most abundant organism in IU (22.65%) and was enriched in IU compared to other ulcer groups. Follow-up samples (n = 31) were obtained from nonhealed ulcers; the average relative abundance of S. pyogenes was 30.11% in not improved ulcers and 0.88% in improved ulcers, suggesting that S. pyogenes in the not improved ulcers may be azithromycin resistant. Catonella morbi was enriched in IU that lacked S. pyogenes As some S. pyogenes and TP strains are macrolide resistant, penicillin may be the drug of choice for CU azithromycin treatment failures. Our study will aid in the design of diagnostic tests and selective therapies for CU.IMPORTANCE Cutaneous ulcers (CU) affect approximately 100,000 children in the tropics each year. While two-thirds of CU are caused by Treponema pallidum subspecies pertenue and Haemophilus ducreyi, the cause(s) of the remaining one-third is unknown. Given the failure of mass drug administration of azithromycin to eradicate CU, the World Health Organization recently proposed an integrated disease management strategy to control CU. Success of this strategy requires determining the unknown cause(s) of CU. By using 16S rRNA gene sequencing of swabs obtained from CU and the skin of asymptomatic children, we identified another possible cause of skin ulcers, Streptococcus pyogenes Although S. pyogenes is known to cause impetigo and cellulitis, this is the first report implicating the organism as a causal agent of CU. Inclusion of S. pyogenes into the integrated disease management plan will improve diagnostic testing and treatment of this painful and debilitating disease of children and strengthen elimination efforts.},
}
@article {pmid33436089,
year = {2021},
author = {Bellas, CM and Sommaruga, R},
title = {Polinton-like viruses are abundant in aquatic ecosystems.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {13},
pmid = {33436089},
issn = {2049-2618},
support = {FWF, M 2299-B32//FWF Austrian Science Fund/ ; },
abstract = {BACKGROUND: Polintons are large mobile genetic elements found in the genomes of eukaryotic organisms that are considered the ancient ancestors of most eukaryotic dsDNA viruses. Originally considered as transposons, they have been found to encode virus capsid genes, suggesting they may actually be integrated viruses; however, an extracellular form has yet to be detected. Recently, circa 25 Polinton-like viruses have been discovered in environmental metagenomes and algal genomes, which shared distantly related genes to both Polintons and virophages (Lavidaviridae). These entities could be the first members of a major class of ancient eukaryotic viruses; however, owing to the lack of available genomes for analysis, information on their global diversity, evolutionary relationships, eukaryotic hosts, and status as free virus particles is limited.<br><br>RESULTS: Here, we analysed the metaviromes of an alpine lake to show that Polinton-like virus genome sequences are abundant in the water column. We identify major capsid protein genes belonging to 82 new Polinton-like viruses and use these to interrogate publicly available metagenomic datasets, identifying 543 genomes and a further 16 integrated into eukaryotic genomes. Using an analysis of shared gene content and major capsid protein phylogeny, we define large groups of Polinton-like viruses and link them to diverse eukaryotic hosts, including a new group of viruses, which possess all the core genes of virophages and infect oomycetes and Chrysophyceae.<br><br>CONCLUSIONS: Our study increased the number of known Polinton-like viruses by 25-fold, identifying five major new groups of eukaryotic viruses, which until now have been hidden in metagenomic datasets. The large enrichment (> 100-fold) of Polinton-like virus sequences in the virus-sized fraction of this alpine lake and the fact that their viral major capsid proteins are found in eukaryotic host transcriptomes support the hypothesis that Polintons in unicellular eukaryotes are viruses. In summary, our data reveals a diverse assemblage of globally distributed viruses, associated with a wide range of unicellular eukaryotic hosts. We anticipate that the methods we have developed for Polinton-like virus detection and the database of over 20,000 genes we present will allow for continued discovery and analysis of these new viral groups. Video abstract.},
}
@article {pmid33436010,
year = {2021},
author = {Liu, J and Liu, C and Yue, J},
title = {Radiotherapy and the gut microbiome: facts and fiction.},
journal = {Radiation oncology (London, England)},
volume = {16},
number = {1},
pages = {9},
pmid = {33436010},
issn = {1748-717X},
support = {81871895//National Natural Science Foundation of China/ ; 2019RC003//Young Taishan Scholars and Academic Promotion Program of Shandong First Medical University/ ; },
abstract = {An ever-growing body of evidence has linked the gut microbiome with both the effectiveness and the toxicity of cancer therapies. Radiotherapy is an effective way to treat tumors, although large variations exist among patients in tumor radio-responsiveness and in the incidence and severity of radiotherapy-induced side effects. Relatively little is known about whether and how the microbiome regulates the response to radiotherapy. Gut microbiota may be an important player in modulating &quot;hot&quot; versus &quot;cold&quot; tumor microenvironment, ultimately affecting treatment efficacy. The interaction of the gut microbiome and radiotherapy is a bidirectional function, in that radiotherapy can disrupt the microbiome and those disruptions can influence the effectiveness of the anticancer treatments. Limited data have shown that interactions between the radiation and the microbiome can have positive effects on oncotherapy. On the other hand, exposure to ionizing radiation leads to changes in the gut microbiome that contribute to radiation enteropathy. The gut microbiome can influence radiation-induced gastrointestinal mucositis through two mechanisms including translocation and dysbiosis. We propose that the gut microbiome can be modified to maximize the response to treatment and minimize adverse effects through the use of personalized probiotics, prebiotics, or fecal microbial transplantation. 16S rRNA sequencing is the most commonly used approach to investigate distribution and diversity of gut microbiome between individuals though it only identifies bacteria level other than strain level. The functional gut microbiome can be studied using methods involving metagenomics, metatranscriptomics, metaproteomics, as well as metabolomics. Multiple '-omic' approaches can be applied simultaneously to the same sample to obtain integrated results. That said, challenges and remaining unknowns in the future that persist at this time include the mechanisms by which the gut microbiome affects radiosensitivity, interactions between the gut microbiome and combination treatments, the role of the gut microbiome with regard to predictive and prognostic biomarkers, the need for multi &quot;-omic&quot; approach for in-depth exploration of functional changes and their effects on host-microbiome interactions, and interactions between gut microbiome, microbial metabolites and immune microenvironment.},
}
@article {pmid33435894,
year = {2021},
author = {Duan, H and Li, X and Mei, A and Li, P and Liu, Y and Li, X and Li, W and Wang, C and Xie, S},
title = {The diagnostic value of metagenomic next⁃generation sequencing in infectious diseases.},
journal = {BMC infectious diseases},
volume = {21},
number = {1},
pages = {62},
pmid = {33435894},
issn = {1471-2334},
support = {81802262//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Although traditional diagnostic techniques of infection are mature and price favorable at present, most of them are time-consuming and with a low positivity. Metagenomic next⁃generation sequencing (mNGS) was studied widely because of identification and typing of all pathogens not rely on culture and retrieving all DNA without bias. Based on this background, we aim to detect the difference between mNGS and traditional culture method, and to explore the relationship between mNGS results and the severity, prognosis of infectious patients.<br><br>METHODS: 109 adult patients were enrolled in our study in Shanghai Tenth People's Hospital from October 2018 to December 2019. The diagnostic results, negative predictive values, positive predictive values, false positive rate, false negative rate, pathogen and sample types were analyzed by using both traditional culture and mNGS methods. Then, the samples and clinical information of 93 patients in the infected group (ID) were collected. According to whether mNGS detected pathogens, the patients in ID group were divided into the positive group of 67 cases and the negative group of 26 cases. Peripheral blood leukocytes, C-reactive protein (CRP), procalcitonin (PCT) and neutrophil counts were measured, and the concentrations of IL-2, IL-4, IL-6, TNF-α, IL-17A, IL-10 and INF-γ in the serum were determined by ELISA. The correlation between the positive detection of pathogens by mNGS and the severity of illness, hospitalization days, and mortality were analyzed.<br><br>RESULTS: 109 samples were assigned into infected group (ID, 92/109, 84.4%), non-infected group (NID, 16/109, 14.7%), and unknown group (1/109, 0.9%). Blood was the most abundant type of samples with 37 cases, followed by bronchoalveolar lavage fluid in 36 cases, tissue, sputum, pleural effusion, cerebrospinal fluid (CSF), pus, bone marrow and nasal swab. In the ID group, the majority of patients were diagnosed with lower respiratory system infections (73/109, 67%), followed by bloodstream infections, pleural effusion and central nervous system infections. The sensitivity of mNGS was significantly higher than that of culture method (67.4% vs 23.6%; P < 0.001), especially in sample types of bronchoalveolar lavage fluid (P = 0.002), blood (P < 0.001) and sputum (P = 0.037), while the specificity of mNGS was not significantly different from culture method (68.8% vs 81.3%; P = 0.41). The number of hospitals stays and 28-day-motality in the positive mNGS group were significantly higher than those in the negative group, and the difference was statistically significant (P < 0.05). Age was significant in multivariate logistic analyses of positive results of mNGS.<br><br>CONCLUSIONS: The study found that mNGS had a higher sensitivity than the traditional method, especially in blood, bronchoalveolar lavage fluid and sputum samples. And positive mNGS group had a higher hospital stay, 28-day-mortality, which means the positive of pathogen nucleic acid sequences detection may be a potential high-risk factor for poor prognosis of adult patients and has significant clinical value. MNGS should be used more in early pathogen diagnosis in the future.},
}
@article {pmid32995839,
year = {2020},
author = {},
title = {Corrigendum to: Gut metagenomics-derived genes as potential biomarkers of Parkinson's disease.},
journal = {Brain : a journal of neurology},
volume = {143},
number = {12},
pages = {e109},
doi = {10.1093/brain/awaa310},
pmid = {32995839},
issn = {1460-2156},
}
@article {pmid33434312,
year = {2021},
author = {Pan, J and Huo, T and Yang, H and Li, Z and Chen, L and Niu, Z and Ni, S and Liu, S},
title = {Metabolic patterns reveal enhanced anammox activity at low-nitrogen conditions in the integrated I-ABR.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {},
number = {},
pages = {},
doi = {10.1002/wer.1511},
pmid = {33434312},
issn = {1554-7531},
abstract = {Substrate concentrations greatly influence bacterial growth and metabolism. However, optimal nitrogen concentrations for anammox bacteria in nitrogen-limited environments remain unclear. Here, we observed enhanced nitrogen metabolism and anabolism of anammox bacteria at low-nitrogen conditions. Efficient nitrogen removal was achieved at ammonium and nitrite influent concentration of 30 mg/L under HRT of 1h, with an average nitrogen removal rate (NRR) of 0.73 kg N/(m3 ·d) in I-ABR composed of four compartments. The highest anammox activity of 6.25 mmol N/ (gVSS·h) was observed in the fourth compartment (C4) with the lowest substrate levels (ammonium and nitrite of 11.6 mg/L and 7 mg/L). This could be resulted from the highest expression level of genes involved in nitrogen metabolism in C4, which was 1.49-1.67 times higher than that in other compartments. Besides, the second compartment (C2) exhibited the most active anabolism at ammonium and nitrite of 17 mg/L and 13 mg/L, respectively, which contributed to the most active amino acid synthesis and thus the highest EPS (1.35 times higher) in C2. This enhanced amino acid auxotrophy between anammox bacteria with heterotrophs, and consequently, heterotrophs thrived and competed for nitrite. These results hint at the potential application of anammox process in micro-polluted water.},
}
@article {pmid33432373,
year = {2021},
author = {Malakar, D and Sarathbabu, S and Borah, P and Kumar, NS},
title = {Fish gill microbiome from India's largest Brahmaputra River-a trans-border biodiversity hotspot region.},
journal = {Environmental monitoring and assessment},
volume = {193},
number = {2},
pages = {56},
doi = {10.1007/s10661-021-08847-z},
pmid = {33432373},
issn = {1573-2959},
support = {No. BT/BI/12/060/2012//Department of Biotechnology, Government of India/ ; },
abstract = {In this study, we sequenced the V3-V4 region of 16S rRNA gene amplicon using paired-end Illumina HiSeq to study the bacterial community in the gills of fish from the bank of the trans-border river of Brahmaputra, Northeast India. Metagenome data consisted of 278,784 reads, 248-bp length, and 56.48% GC content with 85% sequence having a Phred score Q = 30. Community metagenomics revealed a total of 631 genera belonging to 22 different phyla, dominated by Proteobacteria (118,222 features), Firmicutes (101,043 features), Actinobacteria (34,189 features), Bacteroidetes (17,977 features), and Cyanobacteria (2730 features). The bacterial community identified was composed of both pathogenic zoonotic and non-harmful groups. The pathway or functional analysis of the fish gill microbiome exhibited 21 different pathways which also included the pathogenic-related functions. Our data detected a wide group of bacterial communities that will be useful in further isolating and characterizing the pathogenic bacteria from the fish and also to understand the bacterial association in highly consumed fish.},
}
@article {pmid33432175,
year = {2021},
author = {Asnicar, F and Berry, SE and Valdes, AM and Nguyen, LH and Piccinno, G and Drew, DA and Leeming, E and Gibson, R and Le Roy, C and Khatib, HA and Francis, L and Mazidi, M and Mompeo, O and Valles-Colomer, M and Tett, A and Beghini, F and Dubois, L and Bazzani, D and Thomas, AM and Mirzayi, C and Khleborodova, A and Oh, S and Hine, R and Bonnett, C and Capdevila, J and Danzanvilliers, S and Giordano, F and Geistlinger, L and Waldron, L and Davies, R and Hadjigeorgiou, G and Wolf, J and Ordovás, JM and Gardner, C and Franks, PW and Chan, AT and Huttenhower, C and Spector, TD and Segata, N},
title = {Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {33432175},
issn = {1546-170X},
abstract = {The gut microbiome is shaped by diet and influences host metabolism; however, these links are complex and can be unique to each individual. We performed deep metagenomic sequencing of 1,203 gut microbiomes from 1,098 individuals enrolled in the Personalised Responses to Dietary Composition Trial (PREDICT 1) study, whose detailed long-term diet information, as well as hundreds of fasting and same-meal postprandial cardiometabolic blood marker measurements were available. We found many significant associations between microbes and specific nutrients, foods, food groups and general dietary indices, which were driven especially by the presence and diversity of healthy and plant-based foods. Microbial biomarkers of obesity were reproducible across external publicly available cohorts and in agreement with circulating blood metabolites that are indicators of cardiovascular disease risk. While some microbes, such as Prevotella copri and Blastocystis spp., were indicators of favorable postprandial glucose metabolism, overall microbiome composition was predictive for a large panel of cardiometabolic blood markers including fasting and postprandial glycemic, lipemic and inflammatory indices. The panel of intestinal species associated with healthy dietary habits overlapped with those associated with favorable cardiometabolic and postprandial markers, indicating that our large-scale resource can potentially stratify the gut microbiome into generalizable health levels in individuals without clinically manifest disease.},
}
@article {pmid33432149,
year = {2021},
author = {Lee, SH and Cho, SY and Yoon, Y and Park, C and Sohn, J and Jeong, JJ and Jeon, BN and Jang, M and An, C and Lee, S and Kim, YY and Kim, G and Kim, S and Kim, Y and Lee, GB and Lee, EJ and Kim, SG and Kim, HS and Kim, Y and Kim, H and Yang, HS and Kim, S and Kim, S and Chung, H and Moon, MH and Nam, MH and Kwon, JY and Won, S and Park, JS and Weinstock, GM and Lee, C and Yoon, KW and Park, H},
title = {Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {33432149},
issn = {2058-5276},
support = {10067758//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; NRF-2018M3A9F3056902//National Research Foundation of Korea (NRF)/ ; 2018R1C1B6005768//National Research Foundation of Korea (NRF)/ ; NRF-2018R1A2A1A05019794//National Research Foundation of Korea (NRF)/ ; 2015K1A4A3047851//National Research Foundation of Korea (NRF)/ ; 2017R1C1B2011196//National Research Foundation of Korea (NRF)/ ; NRF-2017M3A9F304636//National Research Foundation of Korea (NRF)/ ; 2017-2019//Ewha Womans University (Ewha)/ ; HI17C1076//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; NCC-1911267//National Cancer Center (NCC)/ ; GIST Research Institute (GRI)//Gwangju Institute of Science and Technology (GIST)/ ; },
abstract = {The gut microbiome can influence the development of tumours and the efficacy of cancer therapeutics1-5; however, the multi-omics characteristics of antitumour bacterial strains have not been fully elucidated. In this study, we integrated metagenomics, genomics and transcriptomics of bacteria, and analyses of mouse intestinal transcriptome and serum metabolome data to reveal an additional mechanism by which bacteria determine the efficacy of cancer therapeutics. In gut microbiome analyses of 96 samples from patients with non-small-cell lung cancer, Bifidobacterium bifidum was abundant in patients responsive to therapy. However, when we treated syngeneic mouse tumours with commercial strains of B. bifidum to establish relevance for potential therapeutic uses, only specific B. bifidum strains reduced tumour burden synergistically with PD-1 blockade or oxaliplatin treatment by eliciting an antitumour host immune response. In mice, these strains induced tuning of the immunological background by potentiating the production of interferon-γ, probably through the enhanced biosynthesis of immune-stimulating molecules and metabolites.},
}
@article {pmid33432015,
year = {2021},
author = {Debesa-Tur, G and Pérez-Brocal, V and Ruiz-Ruiz, S and Castillejo, A and Latorre, A and Soto, JL and Moya, A},
title = {Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {391},
pmid = {33432015},
issn = {2045-2322},
support = {AECC 2017-1485//Fundación Científica Asociación Española Contra el Cáncer/ ; AECC 2017-1485//Fundación Científica Asociación Española Contra el Cáncer/ ; AECC 2017-1485//Fundación Científica Asociación Española Contra el Cáncer/ ; AECC 2017-1485//Fundación Científica Asociación Española Contra el Cáncer/ ; },
abstract = {An increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that had developed CRC and had undergone surgical resection. Formalin-fixed paraffin embedded (FFPE) tissue blocks from matched colorectal and normal mucosa were used for genomic DNA extraction with a commercial kit and sequenced by high-throughput sequencing. A metagenomic approach enabled the taxonomic and functional identification of the microbial community and associated genes detected in the specimens. Slightly lower taxonomic diversity was observed in the tumor compared to the non-tumor tissue. Furthermore, the most remarkable differences between tumors and healthy tissue was the significant increase in the genus Fusobacterium in the former, in particular the species F. nucleatum, as well as Camplylobacter or Bacteroides fragilis, in accordance with previous studies of CRC. However, unlike prior studies, the present work is not based on directed detection by qPCR but instead uses a metagenomic approach to retrieve the whole bacterial community, and addresses the additional difficulty of using long-term stored FFPE samples.},
}
@article {pmid33430705,
year = {2021},
author = {Ma, C and Chen, K and Wang, Y and Cen, C and Zhai, Q and Zhang, J},
title = {Establishing a novel colorectal cancer predictive model based on unique gut microbial single nucleotide variant markers.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1-6},
doi = {10.1080/19490976.2020.1869505},
pmid = {33430705},
issn = {1949-0984},
abstract = {Current metagenomic species-based colorectal cancer (CRC) microbial biomarkers may confuse diagnosis because the genetic content of different microbial strains, even those belonging to the same species, may differ from 5% to 30%. Here, a total of 7549 non-redundant single nucleotide variants (SNVs) were annotated in 25 species from 3 CRC cohorts (n = 249). Then, 22 microbial SNV markers that contributed to distinguishing subjects with CRC from healthy subjects were identified by the random forest algorithm to construct a novel CRC predictive model. Excitingly, the predictive model showed high accuracy both in the training (AUC = 75.35%) and validation cohorts (AUC = 73.08%-88.02%). We further explored the specificity of these SNV markers in a broader background by performing a meta-analysis across 4 metabolic disease cohorts. Among these SNV markers, 3 SNVs that were enriched in CRC patients and located in the genomes of Eubacterium rectale and Faecalibacterium prausnitzii were CRC specific (AUC = 72.51%-94.07%).},
}
@article {pmid33428153,
year = {2021},
author = {Zhao, W and Ren, Z and Luo, Y and Cheng, J and Wang, J and Wang, Y and Yang, Z and Yao, X and Zhong, Z and Yang, W and Wu, X},
title = {Metagenomics analysis of the gut microbiome in healthy and bacterial pneumonia forest musk deer.},
journal = {Genes &amp; genomics},
volume = {},
number = {},
pages = {},
pmid = {33428153},
issn = {2092-9293},
support = {2020JDZH0024//The Science and Technology Achievements Transfer Project in 2020 from Scientific Research Institutions of Science and Technology Department of Sichuan Province, Sichuan, China/ ; },
abstract = {BACKGROUND: The forest musk deer (FMD, Moschus berezovskii) is an threatened species in China. Bacterial pneumonia was found to seriously restrict the development of FMD captive breeding. Historical evidence has demonstrated the relationship between immune system and intestinal Lactobacillus in FMD.<br><br>OBJECTIVE: We sought to elucidate the differences in the gut microbiota of healthy and bacterial pneumonia FMD.<br><br>METHODS: The bacterial pneumonia FMD was demonstrated by bacterial and pathological diagnosis, and the gut microbiome of healthy and bacterial pneumonia FMD was sequenced and analysed.<br><br>RESULTS: There are three pathogens (Pseudomonas aeruginosa, Streptococcus equinus and Trueperella pyogenes) isolated from the bacterial pneumonia FMD individuals. Compared with the healthy group, the abundance of Firmicutes and Proteobacteria in the pneumonia group was changed, and a high level of Proteobacteria was found in the pneumonia group. In addition, a higher abundance of Acinetobacter (p = 0.01) was observed in the population of the pneumonia group compared with the healthy group. Several potentially harmful bacteria and disease-related KEGG subsystems were only found in the gut of the bacterial pneumonia group. Analysis of KEGG revealed that many genes related to type IV secretion system, type IV pilus, lipopolysaccharide export system, HTH-type transcriptional regulator/antitoxin MqsA, and ArsR family transcriptional regulator were significantly enriched in the metagenome of the bacterial pneumonia FMD.<br><br>CONCLUSION: Our results demonstrated that the gut microbiome was significantly altered in the bacterial pneumonia group. Overall, our research improves the understanding of the potential role of the gut microbiota in the FMD bacterial pneumonia.},
}
@article {pmid33428003,
year = {2021},
author = {Demirci, H and Kurt-Gur, G and Ordu, E},
title = {Microbiota profiling and screening of the lipase active halotolerant yeasts of the olive brine.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {37},
number = {2},
pages = {23},
pmid = {33428003},
issn = {1573-0972},
abstract = {Searching for novel enzymes that could be active in organic solvents has become an area of interest in recent years. Olive brine naturally provides a suitable environment for the survival of halophilic and acidophilic microorganisms and the resulting genome is thought to be a gene source for determining the halophilic and acidophilic proteins that are active in a non-aqueous organic solvent medium, and so it has been used in several biotechnological and industrial applications. In this study, microbial analysis of natural, cracked green olive brine from the southern region of Turkey has been made by next-generation sequencing of the brine metagenome for the first time in the literature. The number of reads assigned to fungal operational taxonomic units was the highest percentage (73.04%) with the dominant representation of Ascomycota phylum (99% of fungi). Bacterial OTU was 3.56% of the reads and Proteobacteria phylum was 65% of the reads. The lipase production capacity of the yeasts that were grown on the media containing elevated concentrations of NaCl (1-3 M) was determined on a Rhodamine B-including medium. Molecular identification of the selected yeasts was performed and 90% of sequenced yeasts had a high level of similarity with Candida diddensiae, whereas 10% showed similarity to Candida boidinii. The hydrolytic lipase activities using olive oil were analyzed and both yeasts showed cell-bound lipase activity at pH 3.0.},
}
@article {pmid33427933,
year = {2021},
author = {Mulualem, DM and Agbavwe, C and Ogilvie, LA and Jones, BV and Kilcoyne, M and O'Byrne, C and Boyd, A},
title = {Metagenomic identification, purification and characterisation of the Bifidobacterium adolescentis BgaC β-galactosidase.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {33427933},
issn = {1432-0614},
abstract = {Members of the human gut microbiota use glycoside hydrolase (GH) enzymes, such as β-galactosidases, to forage on host mucin glycans and dietary fibres. A human faecal metagenomic fosmid library was constructed and functionally screened to identify novel β-galactosidases. Out of the 16,000 clones screened, 30 β-galactosidase-positive clones were identified. The β-galactosidase gene found in the majority of the clones was BAD_1582 from Bifidobacterium adolescentis, subsequently named bgaC. This gene was cloned with a hexahistidine tag, expressed in Escherichia coli and His-tagged-BgaC was purified using Ni2+-NTA affinity chromatography and size filtration. The enzyme had optimal activity at pH 7.0 and 37 °C, with a wide range of pH (4-10) and temperature (0-40 °C) stability. It required a divalent metal ion co-factor; maximum activity was detected with Mg2+, while Cu2+ and Mn2+ were inhibitory. Kinetic parameters were determined using ortho-nitrophenyl-β-D-galactopyranoside (ONPG) and lactose substrates. BgaC had a Vmax of 107 μmol/min/mg and a Km of 2.5 mM for ONPG and a Vmax of 22 μmol/min/mg and a Km of 3.7 mM for lactose. It exhibited low product inhibition by galactose with a Ki of 116 mM and high tolerance for glucose (66% activity retained in presence of 700 mM glucose). In addition, BgaC possessed transglycosylation activity to produce galactooligosaccharides (GOS) from lactose, as determined by TLC and HPLC analysis. The enzymatic characteristics of B. adolescentis BgaC make it an ideal candidate for dairy industry applications and prebiotic manufacture.Key points• Bifidobacterium adolescentis BgaC β-galactosidase was selected from human faecal metagenome.• BgaC possesses sought-after properties for biotechnology, e.g. low product inhibition.• BgaC has transglycosylation activity producing prebiotic oligosaccharides. Graphical Abstract.},
}
@article {pmid33426245,
year = {2021},
author = {Hoang, HT and Le, DH and Le, TTH and Nguyen, TTN and Chu, HH and Nguyen, NT},
title = {Metagenomic 16S rDNA amplicon data of microbial diversity of guts in Vietnamese humans with type 2 diabetes and nondiabetic adults.},
journal = {Data in brief},
volume = {34},
number = {},
pages = {106690},
doi = {10.1016/j.dib.2020.106690},
pmid = {33426245},
issn = {2352-3409},
abstract = {Type 2 diabetes mellitus (T2DM) is an important public health problem. The knowledge of bacterial communities in the gut of Vietnamese patients with T2DM and non diabetic controls is still insufficient. We report in this article the 16S rDNA amplicon data of the gut microbiomes of Vietnamese patients with T2DM and nondiabetic controls carried out using the Illumina sequencing. This work included 7 patients and 7 controls. A total of 1,627,646 reads were obtained and a total of 13 phyla, 25 classes, 94 genera were revealed. The top three dominant bacterial phyla in all subjects were Firmicutes, Bacteroidetes and Proteobacteria. Significant differences in the relative abundances of the phylum Firmicutes and class Clostridia between patients and controls were observed, suggesting that the reducing of phylum Firmicutes and class Clostridia in the gut may be linked to obesity and T2DM. All sequencing libraries were deposited in the NCBI SRA as BioProject PRJNA668251. The datasets are needed to determine the association between the bacterial composition of the gut and the pathogenesis of T2DM in Vietnamese patients.},
}
@article {pmid33425970,
year = {2020},
author = {Chen, B and Liu, S and Feng, D and Xiao, L and Yang, T and Li, T and Sun, W and Chen, J},
title = {Vitamin A Deficiency in the Early-Life Periods Alters a Diversity of the Colonic Mucosal Microbiota in Rats.},
journal = {Frontiers in nutrition},
volume = {7},
number = {},
pages = {580780},
doi = {10.3389/fnut.2020.580780},
pmid = {33425970},
issn = {2296-861X},
abstract = {Vitamin A deficiency (VAD) remains a public health issue worldwide, affecting pregnant women and children. The early-life microbiota is a potentially effective intervention target for modulating immune and metabolic development of the host. This paper investigates the effects of VAD during different life periods on the structure of the colonic mucosa microbiota in adolescent rats. The results showed that the concentrations of serum retinol were > ~1.05 μmol/L in maternal VA normal (VAN)rats and < 0.7 μmol/L in maternal VAD rats, while the serum retinol levels were higher than 0.7 μmol/L in the pups of the VAN group and below 0.5 μmol/L in the pups of the VAD group. Compared to the offspring persistent with VAN from embryonic stage (group A), all the remaining groups exhibited an increased ratio of Firmicutes/Bacteroidetes abundance. A metagenome analysis (LEfSe) and a differentially abundant features approach using Metastats for genus abundances revealed that Diaphorobacter and Psychrobacter were increased in the offspring persistent with VAD from embryonic stage (group B);Bifidobacterium was decreased and Staphylococcus was increased in the offspring with VAD after weaning (group C); Propionibacterium and Enterobacter were increased significantly in the offspring with VAD during gestation(group E); and Ochrobactrum was increased in group B and the offspring with VAD during gestation and lactation(group D). Faecalibacterium abundance was significantly and positively related to serum retinol levels, while that of Staphylococcus was significantly and negatively correlated with serum retinol levels. VAD in different life periods can alter the gut microbiome in rats, but VAD in the early-life periods (especially gestation and/or lactation) leads to a diversity of the colonic mucosal microbiota in adolescent rats as well as an imbalance of the ratio between Firmicutes and Bacteroidetes. The early-life period may become a time window of VA intervention to improve intestinal microbiota caused by VA deficiency, but the specific mechanism requires more in-depth research.},
}
@article {pmid33425781,
year = {2020},
author = {Komatsu, K and Shiba, T and Takeuchi, Y and Watanabe, T and Koyanagi, T and Nemoto, T and Shimogishi, M and Shibasaki, M and Katagiri, S and Kasugai, S and Iwata, T},
title = {Discriminating Microbial Community Structure Between Peri-Implantitis and Periodontitis With Integrated Metagenomic, Metatranscriptomic, and Network Analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {596490},
doi = {10.3389/fcimb.2020.596490},
pmid = {33425781},
issn = {2235-2988},
abstract = {Peri-implantitis and periodontitis are both polymicrobial diseases induced by subgingival plaque accumulation, with some differing clinical features. Studies on the microbial and gene transcription activity of peri-implantitis microbiota are limited. This study aimed to verify the hypothesis that disease-specific microbial and gene transcription activity lead to disease-specific clinical features, using an integrated metagenomic, metatranscriptomic, and network analysis. Metagenomic data in peri-implantitis and periodontitis were obtained from the same 21 subjects and metatranscriptomic data from 12 subjects were obtained from a database. The microbial co-occurrence network based on metagenomic analysis had more diverse species taxa and correlations than the network based on the metatranscriptomic analysis. Solobacterium moorei and Prevotella denticola had high activity and were core species taxa specific to peri-implantitis in the co-occurrence network. Moreover, the activity of plasmin receptor/glyceraldehyde-3-phosphate dehydrogenase genes was higher in peri-implantitis. These activity differences may increase complexity in the peri-implantitis microbiome and distinguish clinical symptoms of the two diseases. These findings should help in exploring a novel biomarker that assist in the diagnosis and preventive treatment design of peri-implantitis.},
}
@article {pmid33425763,
year = {2020},
author = {El Jaddaoui, I and Allali, I and Sehli, S and Ouldim, K and Hamdi, S and Al Idrissi, N and Nejjari, C and Amzazi, S and Bakri, Y and Ghazal, H},
title = {Cancer Omics in Africa: Present and Prospects.},
journal = {Frontiers in oncology},
volume = {10},
number = {},
pages = {606428},
doi = {10.3389/fonc.2020.606428},
pmid = {33425763},
issn = {2234-943X},
abstract = {During the last century, cancer biology has been arguably one of the most investigated research fields. To gain deeper insight into cancer mechanisms, scientists have been attempting to integrate multi omics data in cancer research. Cancer genomics, transcriptomics, metabolomics, proteomics, and metagenomics are the main multi omics strategies used currently in the diagnosis, prognosis, treatment, and biomarker discovery in cancer. In this review, we describe the use of different multi omics strategies in cancer research in the African continent and discuss the main challenges facing the implementation of these approaches in African countries such as the lack of training programs in bioinformatics in general and omics strategies in particular and suggest paths to address deficiencies. As a way forward, we advocate for the establishment of an &quot;African Cancer Genomics Consortium&quot; to promote intracontinental collaborative projects and enhance engagement in research activities that address indigenous aspects for cancer precision medicine.},
}
@article {pmid33424798,
year = {2020},
author = {Zhou, S and Luo, R and Gong, G and Wang, Y and Gesang, Z and Wang, K and Xu, Z and Suolang, S},
title = {Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan Pig.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {595066},
doi = {10.3389/fmicb.2020.595066},
pmid = {33424798},
issn = {1664-302X},
abstract = {Tibetan pig is an important domestic mammal, providing products of high nutritional value for millions of people living in the Qinghai-Tibet Plateau. The genomes of mammalian gut microbiota encode a large number of carbohydrate-active enzymes, which are essential for the digestion of complex polysaccharides through fermentation. However, the current understanding of microbial degradation of dietary carbohydrates in the Tibetan pig gut is limited. In this study, we produced approximately 145 gigabases of metagenomic sequence data for the fecal samples from 11 Tibetan pigs. De novo assembly and binning recovered 322 metagenome-assembled genomes taxonomically assigned to 11 bacterial phyla and two archaeal phyla. Of these genomes, 191 represented the uncultivated microbes derived from novel prokaryotic taxa. Twenty-three genomes were identified as metagenomic biomarkers that were significantly abundant in the gut ecosystem of Tibetan pigs compared to the other low-altitude relatives. Further, over 13,000 carbohydrate-degrading genes were identified, and these genes were more abundant in some of the genomes within the five principal phyla: Firmicutes, Bacteroidetes, Spirochaetota, Verrucomicrobiota, and Fibrobacterota. Particularly, three genomes representing the uncultivated Verrucomicrobiota encode the most abundant degradative enzymes in the fecal microbiota of Tibetan pigs. These findings should substantially increase the phylogenetic diversity of specific taxonomic clades in the microbial tree of life and provide an expanded repertoire of biomass-degrading genes for future application to microbial production of industrial enzymes.},
}
@article {pmid33424792,
year = {2020},
author = {Huyben, D and Roehe, BK and Bekaert, M and Ruyter, B and Glencross, B},
title = {Dietary Lipid:Protein Ratio and n-3 Long-Chain Polyunsaturated Fatty Acids Alters the Gut Microbiome of Atlantic Salmon Under Hypoxic and Normoxic Conditions.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {589898},
doi = {10.3389/fmicb.2020.589898},
pmid = {33424792},
issn = {1664-302X},
abstract = {Researchers have adjusted dietary lipid:protein ratios and n-3 long-chain polyunsaturated fatty acids (LC-PUFA) to optimize the growth performance of Atlantic salmon. However, dietary impacts on the gut microbiome are lacking, especially under varying environmental conditions. To examine this response, post-smolt salmon (184 ± 5 g) were fed diets with lipid:protein ratios considered low (180, 570 g/kg) and high (230, 460 g/kg) along with low and high levels of n-3 LC-PUFA (7 or 14 g/kg) while fish were reared under low and high levels of dissolved oxygen (6.7 or 8.0 mg/L). At day 0, 35 and 116, digesta in the distal intestine were collected and analyzed for viable counts and 16S ribosomal RNA (rRNA) genes (V4 region) using Illumina MiSeq. The reduction in oxygen had negligible effects, except on viable plate counts of total bacteria and an initial effect on beta-diversity. In contrast, the high lipid (HL) diets had an increased alpha-diversity (e.g., Shannon and Chao-1) at day 0 and day 35 whereas high n-3 diets suppressed these indices at day 116. Generally, a reduction in alpha-diversity was observed over time and an interaction between lipid:protein ratio x n-3 was found. Between diets, beta-diversity and phyla abundance were similar as both Proteobacteria (44%) and Firmicutes (21%) dominated. However, at the genus level Aliivibrio, Streptococcus, Weissella, and Lactobacillus, were associated with low lipid (LL) diets while the high lipid diets were associated with less abundant bacteria, e.g., Chromohalobacter. At day 116, the relative abundance of the Tenericutes phylum increased 10-fold (36%). Fish fed the high lipid diet with high n-3 had reduced alpha-diversity, lowest abundance of lactic acid bacteria, and highest abundance of Mycoplasma, which may indicate a less healthy gut microbiome. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed that saturated and unsaturated fatty acid biosynthesis pathways were several folds higher in fish fed the high lipid diet, possibly to compensate for the lack of dietary n-3. In summary, our results show that the viable plate counts, alpha-diversity, beta-diversity, and predictive function of gut bacteria in Atlantic salmon post-smolts are influenced by dietary lipid:protein ratio and n-3 LC-PUFA over several time points with little effect by dissolved oxygen.},
}
@article {pmid33424787,
year = {2020},
author = {Figueroa-Gonzalez, PA and Bornemann, TLV and Adam, PS and Plewka, J and Révész, F and von Hagen, CA and Táncsics, A and Probst, AJ},
title = {Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {587782},
doi = {10.3389/fmicb.2020.587782},
pmid = {33424787},
issn = {1664-302X},
abstract = {Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.},
}
@article {pmid33424783,
year = {2020},
author = {Song, J and Li, Q and Everaert, N and Liu, R and Zheng, M and Zhao, G and Wen, J},
title = {Dietary Inulin Supplementation Modulates Short-Chain Fatty Acid Levels and Cecum Microbiota Composition and Function in Chickens Infected With Salmonella.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {584380},
doi = {10.3389/fmicb.2020.584380},
pmid = {33424783},
issn = {1664-302X},
abstract = {The current study investigated the effects of inulin on the gut microbiota, microbiome functions, and short-chain fatty acids (SCFAs) levels in specific pathogen-free (SPF) chickens infected with Salmonella enteritidis (SE). SPF Arbor Acres chickens (n = 240, 1-day-old) were divided into four groups: a control group (CON) fed a basal diet without inulin supplementation or SE infection, and three groups fed a basal diet supplemented with inulin 0, 0.5, and 1% (SE, 0.5%InSE, 1%InSE, respectively) up to 28-days-old, followed by SE challenge at 28 days of age. Cecal SCFA contents and microbiome composition and function were analyzed at 1-day post-infection. The results showed that SE infection significantly decreased cecal butyrate concentrations compared with the CON group (p < 0.05), while inulin supplementation reversed these changes compared with the SE group (p < 0.05). Inulin supplementation at 1% significantly increased the abundances of Lactobacillus and Streptococcus, and significantly decreased the abundances of Subdoligranulum and Sellimonas compared with the SE group (p < 0.05). The functional profiles of microbial communities based on metagenomic sequencing analysis showed that SE infection significantly increased the abundances of pathways related to carbohydrate metabolism, amino acid metabolism, energy metabolism, metabolism of cofactors and vitamins, and glycan biosynthesis and metabolism (p < 0.05), and significantly decreased the abundances of pathways related to nucleotide metabolism, translation, and replication and repair compared with the CON group (p < 0.05), and these effects were reversed by inulin supplementation (0.5 and 1%) (p < 0.05). In conclusion, inulin modulated the dysbiosis induced by SE infection via affecting SCFA metabolism and microbial functional profiles.},
}
@article {pmid33424778,
year = {2020},
author = {Chen, M and Liu, S and Imam, KMSU and Sun, L and Wang, Y and Gu, T and Wen, B and Xin, F},
title = {The Effect of Xylooligosaccharide, Xylan, and Whole Wheat Bran on the Human Gut Bacteria.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {568457},
doi = {10.3389/fmicb.2020.568457},
pmid = {33424778},
issn = {1664-302X},
abstract = {Wheat bran is a cereal rich in dietary fibers that have high levels of ferulic acid, which has prebiotic effects on the intestinal microbiota and the host. Herein we explored the effect of xylooligosaccharide, xylan, and whole wheat bran on the human gut bacteria and screened for potential ferulic acid esterase genes. Using in vitro fermentation, we analyzed the air pressure, pH-value, and short-chain fatty acid levels. We also performed 16S rRNA gene and metagenomic sequencing. A Venn diagram analysis revealed that 80% of the core operational taxonomic units (OTUs) were shared among the samples, and most of the xylooligosaccharide treatment core OTUs (319/333 OTUs) were shared with the other two treatments' core OTUs. A significant difference analysis revealed that the relative abundance of Dorea, Bilophila, and Sulfurovum in wheat bran treatment was higher than that in xylan and xylooligosaccharide treatments. The clusters of orthologous groups of proteins functional composition of all samples was similar to the microbiota composition of the control. Using metagenomic sequencing, we revealed seven genes containing the conserved residues, Gly-X-Ser-X-Gly, and the catalytic triad, Ser-His-Asp, which are thus potential ferulic acid esterase genes. All the results indicate that xylan and/or xylooligosaccharide, the main dietary fibers in wheat bran, plays a major role in in vitro fermentation by the human gut microbiota.},
}
@article {pmid33424650,
year = {2020},
author = {Zhao, HJ and Luo, X and Shi, YC and Li, JF and Pan, F and Ren, RR and Peng, LH and Shi, XY and Yang, G and Wang, J and Hu, LY and Zou, LP and Yang, YS},
title = {The Efficacy of Fecal Microbiota Transplantation for Children With Tourette Syndrome: A Preliminary Study.},
journal = {Frontiers in psychiatry},
volume = {11},
number = {},
pages = {554441},
doi = {10.3389/fpsyt.2020.554441},
pmid = {33424650},
issn = {1664-0640},
abstract = {Therapies for Tourette syndrome (TS) are insufficient, and novel therapies are needed. Fecal microbiota transplantation (FMT) has been a potential therapy for several neurological diseases. Here, we report a preliminary study to investigate the effects of FMT on patients with TS. Five patients with TS received a single administration of FMT via endoscopy. Tic symptoms were assessed by Yale Global Tic Severity Scale-Total Tic Score (YGTSS-TTS) and adverse effects were recorded at week 8 following FMT. Lipopolysaccharide (LPS) levels and 14 cytokines levels were measured. The microbiota profile in feces were analyzed by shotgun metagenomics. Four patients (4/5) responded positively to FMT (YGTSS-TTS reduction rate >25%) at week 8 with high safety. The levels of LPS and cytokines varied after FMT. FMT shifted the composition of the gut microbiota in patients close to that of the donor and continuously changed the abundance of Bacteroides coprocola, Dialister succinatiphilus and Bacteroides vulgatus. The restoration of B.coprocola was correlated with the improvement in tic symptoms (Spearman R = -0.900, P = 0.037). In conclusion, FMT was indicated a potential effective and safe alternative for patients with TS. However, larger clinical trials are needed to confirm the influence of microbiota in TS. Trial Registration: chictr.org.cn Identifier: ChiCTR-IIR-17011871, URL: http://www.chictr.org.cn/showproj.aspx?proj=19941.},
}
@article {pmid33424158,
year = {2020},
author = {Ramadurai, S and Balasundaram, U},
title = {Rhizomicrobiomics of Caesalpinia bonducella, a wonder plant for PCOS treatment.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {26},
number = {12},
pages = {2453-2463},
doi = {10.1007/s12298-020-00915-x},
pmid = {33424158},
issn = {0971-5894},
abstract = {Plant and rhizobacterial interactions contribute partly to a plant's medicinal properties and are well studied through metagenomics. In this study, 16S rDNA, 18S rDNA, and ITS meta-sequencing were performed using the genomic DNA obtained from the rhizosphere of Caesalpinia bonducella-a medicinal shrub widely used to treat polycystic ovary syndrome (PCOS). Of the 665 Operational Taxonomic Units (OTUs) obtained from 16S rDNA sequencing, 23.9% comprised of microbes that increase the therapeutic value of plants (Bacillus, Paenibacillus), 6.4% belonged to stress and drought tolerant microbes (Pseudomonas, Rhizobium, Serratia), 8% belonged to plant-growth promoting rhizobacteria-predominantly Proteobacteria, and Firmicutes and the remaining were the microbes performing various other functions. Alpha diversity indexing by GAIA-metagenomics tool revealed the presence of a highly diverse group of microbes in the rhizosphere of C. bonducella; Chao.1 index (665), Shannon Weiner index (3.53), Simpson index (0.83) and Fisher index (106.13). The highly diverse microbes lingering around the roots of C. bonducella could possibly be due to a strong symbiotic association with the plant; root exudates nourish the microbes and the microbes in turn enrich the medicinal value of the plant.},
}
@article {pmid33046719,
year = {2020},
author = {Forsman, ZH and Ritson-Williams, R and Tisthammer, KH and Knapp, ISS and Toonen, RJ},
title = {Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {16995},
pmid = {33046719},
issn = {2045-2322},
mesh = {Animals ; Anthozoa/*physiology ; Biological Evolution ; Coral Reefs ; Hawaii ; Host Adaptation ; Metagenomics/*methods ; Species Specificity ; Symbiosis/*genetics ; },
abstract = {The 'species' is a key concept for conservation and evolutionary biology, yet the lines between population and species-level variation are often blurred, especially for corals. The 'Porites lobata species complex' consists of branching and mounding corals that form reefs across the Pacific. We used reduced representation meta-genomic sequencing to examine genetic relationships within this species complex and to identify candidate loci associated with colony morphology, cryptic genetic structure, and apparent bleaching susceptibility. We compared existing Porites data with bleached and unbleached colonies of the branching coral P. compressa collected in Kāne'ohe Bay Hawai'i during the 2015 coral bleaching event. Loci that mapped to coral, symbiont, and microbial references revealed genetic structure consistent with recent host-symbiont co-evolution. Cryptic genetic clades were resolved that previous work has associated with distance from shore, but no genetic structure was associated with bleaching. We identified many candidate loci associated with morphospecies, including candidate host and symbiont loci with fixed differences between branching and mounding corals. We also found many loci associated with cryptic genetic structure, yet relatively few loci associated with bleaching. Recent host-symbiont co-evolution and rapid diversification suggests that variation and therefore the capacity of these corals to adapt may be underappreciated.},
}
@article {pmid32788589,
year = {2020},
author = {Soriano-Lerma, A and Pérez-Carrasco, V and Sánchez-Marañón, M and Ortiz-González, M and Sánchez-Martín, V and Gijón, J and Navarro-Mari, JM and García-Salcedo, JA and Soriano, M},
title = {Influence of 16S rRNA target region on the outcome of microbiome studies in soil and saliva samples.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {13637},
pmid = {32788589},
issn = {2045-2322},
mesh = {Bacteria/*genetics/growth &amp; development ; Computational Biology ; DNA, Bacterial/*analysis/genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/*analysis/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA/methods ; Soil/*chemistry ; },
abstract = {Next generation sequencing methods are widely used in evaluating the structure and functioning of microbial communities, especially those centered on 16S rRNA subunit. Since Illumina Miseq, the most used sequencing platform, does not allow the full sequencing of 16S rRNA gene, this study aims to evaluate whether the choice of different target regions might affect the outcome of microbiome studies regarding soil and saliva samples. V1V3, V3V4, V4V5 and V6V8 domains were studied, finding that while some regions showed differences in the detection of certain bacterial taxa and in the calculation of alpha diversity, especially in soil samples, the overall effect did not compromise the differentiation of any sample type in terms of taxonomic analysis at the genus level. 16S rRNA target regions did affect the detection of specific bacteria related to soil quality and development, and microbial genera used as health biomarkers in saliva. V1V3 region showed the closest similarity to internal sequencing control mock community B, suggesting it might be the most preferable choice regarding data reliability.},
}
@article {pmid31954373,
year = {2020},
author = {Duan, C and Kuang, L and Xiang, X and Zhang, J and Zhu, Y and Wu, Y and Yan, Q and Liu, L and Li, T},
title = {Activated Drp1-mediated mitochondrial ROS influence the gut microbiome and intestinal barrier after hemorrhagic shock.},
journal = {Aging},
volume = {12},
number = {2},
pages = {1397-1416},
pmid = {31954373},
issn = {1945-4589},
mesh = {Animals ; Biomarkers ; Disease Models, Animal ; Dynamins/*genetics/metabolism ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Intestinal Mucosa/*metabolism/*microbiology ; Male ; Metabolomics/methods ; Metagenomics/methods ; Mice ; Mitochondria/*genetics/*metabolism ; Permeability ; RNA, Ribosomal, 16S/genetics ; Reactive Oxygen Species/*metabolism ; Shock, Hemorrhagic/etiology/*metabolism ; },
abstract = {A role of the mitochondrial dynamin-related protein (Drp1) on gut microbiome composition and intestinal barrier function after hemorrhagic shock has not been identified previously and thus addressed in this study. Here, we used a combination of 16S rRNA gene sequencing and mass spectrometry-based metabolomics profiling in WT and Drp1 KO mouse models to examine the functional impact of activated Drp1 on the gut microbiome as well as mitochondrial metabolic regulation after hemorrhagic shock. Our data showed that changes in mitochondrial Drp1 activity participated in the regulation of intestinal barrier function after hemorrhagic shock. Activated Drp1 significantly perturbed gut microbiome composition in the Bacteroidetes phylum. The abundance of short-chain fatty acid (SCFA) producing microbes, such as Bacteroides, Butyricimonas and Odoribacter, was markedly decreased in mice after shock, and was inversely correlated with both the distribution of the tight junction protein ZO1 and intestinal permeability. Together, these data suggest that Drp1 activation perturbs the gut microbiome community and SCFA production in a ROS-specific manner and thereby substantially disturbs tight junctions and intestinal barrier function after hemorrhagic shock. Our findings provide novel insights for targeting Drp1-mediated mitochondrial function as well as the microbiome in the treatment of intestinal barrier dysfunction after shock.},
}
@article {pmid31907339,
year = {2020},
author = {Wang, QJ and Shen, YE and Wang, X and Fu, S and Zhang, X and Zhang, YN and Wang, RT},
title = {Concomitant memantine and Lactobacillus plantarum treatment attenuates cognitive impairments in APP/PS1 mice.},
journal = {Aging},
volume = {12},
number = {1},
pages = {628-649},
pmid = {31907339},
issn = {1945-4589},
mesh = {Alzheimer Disease/*complications/etiology/metabolism ; Animals ; Animals, Genetically Modified ; Biomarkers ; Choline/administration &amp; dosage ; Cognitive Dysfunction/*etiology/*therapy ; Dietary Supplements ; Disease Models, Animal ; Gastrointestinal Microbiome ; *Lactobacillus plantarum ; Male ; Memantine/*pharmacology ; Metagenomics/methods ; Mice ; Probiotics ; Pyramidal Cells/metabolism ; },
abstract = {Trimethylamine-N-oxide (TMAO) is a gut microbial metabolite that promotes Alzheimer's disease (AD) progression. Given that probiotics can alleviate AD symptoms by inhibiting the synthesis of TMAO, here we investigated the correlation between TMAO and cognitive deterioration by measuring TMAO levels in the plasma of choline-treated APP/PS1 mice (an AD mouse model) with and without probiotic treatments. We found that declines in L.plantarum in the gut were associated with cognitive impairment. Moreover, 12-weeks of treatment with memantine plus L. plantarum ameliorated cognitive deterioration, decreased Αβ levels in the hippocampus, and protected neuronal integrity and plasticity. These effects were accompanied by reductions in TMAO synthesis and neuroinflammation. These experiments demonstrate that L. plantarum augments the beneficial therapeutic effects of memantine treatment in APP/PS1 mice by remodeling the intestinal microbiota, inhibiting the synthesis of TMAO, and reducing clusterin levels. Our results thus highlight intestinal microbiota as a potential therapeutic target to decrease the risk of AD.},
}
@article {pmid31905172,
year = {2020},
author = {Diling, C and Longkai, Q and Yinrui, G and Yadi, L and Xiaocui, T and Xiangxiang, Z and Miao, Z and Ran, L and Ou, S and Dongdong, W and Yizhen, X and Xujiang, Y and Yang, BB and Qingping, W},
title = {CircNF1-419 improves the gut microbiome structure and function in AD-like mice.},
journal = {Aging},
volume = {12},
number = {1},
pages = {260-287},
pmid = {31905172},
issn = {1945-4589},
mesh = {Alzheimer Disease/etiology ; Animals ; Brain/*metabolism ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; *Homeostasis ; Male ; Metagenomics/methods ; Mice ; Mice, Transgenic ; RNA, Circular/chemistry ; },
abstract = {Our pre-experiments found that the brain circRNA sequence profiles and gut microbiota in AD-like mice were changed, as circNF1-419 could enhance autophagy to ameliorate senile dementia in AD-like mice, so we conclude that there might some connections between circRNA and gut microbiome. Therefore, we use the over-expressed circNF1-419 adeno-associated virus (AAV) animal system with the aim of identifying possible connections. Our results showed that over-expression of circNF1-419 in brain not only influenced the cholinergic system of brain, but also changed the gut microbiota composition as the Candidatus Arthromitus, Lachnospiraceae FCS020 group, Lachnospiraceae UCG-006, and [Eubacterium] xylanophilum group, and the intestinal homeostasis and physiology, and even the gut microbiota trajectory in new born mice. These findings demonstrate a link between circRNA and gut microbiome, enlarge the 'microbiome- transcriptome' linkage library and provide more information on gut-brain axis.},
}
@article {pmid33423396,
year = {2021},
author = {Piñol, J},
title = {Genotype by Sequencing: an alternative new method to amplicon metabarcoding and shotgun metagenomics for the assessment of eukaryote biodiversity.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13320},
pmid = {33423396},
issn = {1755-0998},
abstract = {The use of high-throughput DNA-sequencing (HTS) has revolutionised the assessment of biodiversity in plant and animal communities. There are two main approaches to estimate the identity and the relative species abundance (RSA) in complex mixtures using HTS: amplicon metabarcoding and shotgun metagenomics. While amplicon metabarcoding targets one or a few genomic regions, shotgun metagenomics randomly explores the genome of the species. In this issue of Molecular Ecology Resources, Wagemaker et al. (2021) present a new method, multi-species Genotyping by Sequencing (msGBS), as an alternative middle ground between metabarcoding and metagenomics. They apply the technique to mixtures of plant roots and report the remarkable capacity of msGBS to estimate the RSA. If validated in other labs and biological communities, msGBS might become a third method to explore the biodiversity of biological communities, especially of plants, where current techniques are struggling to get sufficient taxonomic resolution.},
}
@article {pmid33422963,
year = {2020},
author = {Pérez-Cataluña, A and Cuevas-Ferrando, E and Randazzo, W and Sánchez, G},
title = {Bias of library preparation for virome characterization in untreated and treated wastewaters.},
journal = {The Science of the total environment},
volume = {767},
number = {},
pages = {144589},
doi = {10.1016/j.scitotenv.2020.144589},
pmid = {33422963},
issn = {1879-1026},
abstract = {The use of metagenomics for virome characterization and its implementation for wastewater analyses, including wastewater-based epidemiology, has increased in the last years. However, the lack of standardized methods can led to highly different results. The aim of this work was to analyze virome profiles in upstream and downstream wastewater samples collected from four wastewater treatment plants (WWTPs) using two different library preparation kits. Viral particles were enriched from wastewater concentrates using a filtration and nuclease digestion procedure prior to total nucleic acid (NA) extraction. Sequencing was performed using the ScriptSeq v2 RNA-Seq (LS) and the NEBNext Ultra II RNA (NB) library preparation kits. Cleaned reads and contigs were annotated using a curated in-house database composed by reads assigned to viruses at NCBI. Significant differences in viral families and in the ratio of detection were shown between the two library kits used. The use of LS library showed Virgaviridae, Microviridae and Siphoviridae as the most abundant families; while Ackermannviridae and Helleviridae were highly represented within the NB library. Additionally, the two sequencing libraries produced outcomes that differed in the detection of viral indicators. These results highlighted the importance of library selection for studying viruses in untreated and treated wastewater. Our results underline the need for further studies to elucidate the influence of sequencing procedures in virome profiles in wastewater matrices in order to improve the knowledge of the virome in the water environment.},
}
@article {pmid33422504,
year = {2021},
author = {Tan, SM and Ismail, MH and Cao, B},
title = {Biodiversity of Magnetotactic Bacteria in the tropical marine environment of Singapore revealed by metagenomic analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {110714},
doi = {10.1016/j.envres.2021.110714},
pmid = {33422504},
issn = {1096-0953},
abstract = {Most studies on the diversity of magnetotactic bacteria (MTB) have been conducted on samples obtained from the Northern or the Southern hemispheres. The diversity of MTB in tropical Asia near the geo-equator, with a close-to-zero geomagnetic inclination, weak magnetic field and constantly high seawater temperature has never been explored. This study aims to decipher the diversity of MTB in the marine environment of Singapore through shotgun metagenomics. Although MTB has been acknowledged to be ubiquitous in aquatic environments, we did not observe magnetotactic behaviour in the samples. However, we detected the presence and determined the diversity of MTB through bioinformatic analyses. Metagenomic analysis suggested majority of the MTB in the seafloor sediments represents novel MTB taxa that cannot be classified at the species level. The relative abundance of MTB (∼0.2-1.69%) in the samples collected from the marine environment of Singapore was found to be substantially lower than studies for other regions. In contrast to other studies, the genera Magnetovibrio and Desulfamplus, but not Magnetococcus, were the dominant MTB. Additionally, we recovered 3 MTB genomic bins that are unclassified at the species level, with Magnetovibrio blakemorei being the closest-associated genome. All the recovered genomic bins contain homologs of at least 5 of the 7 mam genes but lack homologs for mamI, a membrane protein suggested to take part in the magenetosome invagination. This study fills in the knowledge gap of MTB biodiversity in the tropical marine environment near the geo-equator. Our findings will facilitate future research efforts aiming to unravel the ecological roles of MTB in the tropical marine environments as well as to bioprospecting novel MTB that have been adapted to tropical marine environments for biotechnological applications.},
}
@article {pmid33422152,
year = {2021},
author = {Gardiner, LJ and Haiminen, N and Utro, F and Parida, L and Seabolt, E and Krishna, R and Kaufman, JH},
title = {Re-purposing software for functional characterization of the microbiome.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {4},
pmid = {33422152},
issn = {2049-2618},
support = {STFC Hartree Centre's Innovation Return on Research programme//Department for Business, Energy and Industrial Strategy/ ; },
abstract = {BACKGROUND: Widespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows and software. For analysis of the microbiome, workflows typically begin with taxonomic classification of the microorganisms that are present in a given environment. Additional investigation is then required to uncover the functionality of the microbial community, in order to characterize its currently or potentially active biological processes. Such functional analysis of metagenomic data can be computationally demanding for high-throughput sequencing experiments. Instead, we can directly compare sequencing reads to a functionally annotated database. However, since reads frequently match multiple sequences equally well, analyses benefit from a hierarchical annotation tree, e.g. for taxonomic classification where reads are assigned to the lowest taxonomic unit.<br><br>RESULTS: To facilitate functional microbiome analysis, we re-purpose well-known taxonomic classification tools to allow us to perform direct functional sequencing read classification with the added benefit of a functional hierarchy. To enable this, we develop and present a tree-shaped functional hierarchy representing the molecular function subset of the Gene Ontology annotation structure. We use this functional hierarchy to replace the standard phylogenetic taxonomy used by the classification tools and assign query sequences accurately to the lowest possible molecular function in the tree. We demonstrate this with simulated and experimental datasets, where we reveal new biological insights.<br><br>CONCLUSIONS: We demonstrate that improved functional classification of metagenomic sequencing reads is possible by re-purposing a range of taxonomic classification tools that are already well-established, in conjunction with either protein or nucleotide reference databases. We leverage the advances in speed, accuracy and efficiency that have been made for taxonomic classification and translate these benefits for the rapid functional classification of microbiomes. While we focus on a specific set of commonly used methods, the functional annotation approach has broad applicability across other sequence classification tools. We hope that re-purposing becomes a routine consideration during bioinformatic resource development. Video abstract.},
}
@article {pmid33422151,
year = {2021},
author = {Tingley, JP and Low, KE and Xing, X and Abbott, DW},
title = {Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues.},
journal = {Biotechnology for biofuels},
volume = {14},
number = {1},
pages = {16},
pmid = {33422151},
issn = {1754-6834},
support = {J-002262//Agriculture and Agri-Food Canada/ ; J-001589//Agriculture and Agri-Food Canada/ ; 2019H001R//Alberta Agriculture and Forestry/ ; },
abstract = {The production of biofuels as an efficient source of renewable energy has received considerable attention due to increasing energy demands and regulatory incentives to reduce greenhouse gas emissions. Second-generation biofuel feedstocks, including agricultural crop residues generated on-farm during annual harvests, are abundant, inexpensive, and sustainable. Unlike first-generation feedstocks, which are enriched in easily fermentable carbohydrates, crop residue cell walls are highly resistant to saccharification, fermentation, and valorization. Crop residues contain recalcitrant polysaccharides, including cellulose, hemicelluloses, pectins, and lignin and lignin-carbohydrate complexes. In addition, their cell walls can vary in linkage structure and monosaccharide composition between plant sources. Characterization of total cell wall structure, including high-resolution analyses of saccharide composition, linkage, and complex structures using chromatography-based methods, nuclear magnetic resonance, -omics, and antibody glycome profiling, provides critical insight into the fine chemistry of feedstock cell walls. Furthermore, improving both the catalytic potential of microbial communities that populate biodigester reactors and the efficiency of pre-treatments used in bioethanol production may improve bioconversion rates and yields. Toward this end, knowledge and characterization of carbohydrate-active enzymes (CAZymes) involved in dynamic biomass deconstruction is pivotal. Here we overview the use of common &quot;-omics&quot;-based methods for the study of lignocellulose-metabolizing communities and microorganisms, as well as methods for annotation and discovery of CAZymes, and accurate prediction of CAZyme function. Emerging approaches for analysis of large datasets, including metagenome-assembled genomes, are also discussed. Using complementary glycomic and meta-omic methods to characterize agricultural residues and the microbial communities that digest them provides promising streams of research to maximize value and energy extraction from crop waste streams.},
}
@article {pmid33421879,
year = {2020},
author = {Sun, Y and Cao, N and Duan, C and Wang, Q and Ding, C and Wang, J},
title = {Selection of antibiotic resistance genes on biodegradable and non-biodegradable microplastics.},
journal = {Journal of hazardous materials},
volume = {409},
number = {},
pages = {124979},
doi = {10.1016/j.jhazmat.2020.124979},
pmid = {33421879},
issn = {1873-3336},
abstract = {Growing evidence have demonstrated that microplastics in the marine ecosystem can provide novel substrates for biofilm formation, potentially facilitating the spread of antibiotic resistance. However, the occurrence of antibiotic resistance genes (ARGs) in the biofilm on microplastics has not been fully explored. This study used the metagenomic data of biodegradable and non-biodegradable microplastics staged at a coastal lagoon in the northern Gulf of Mexico to profile the ARGs and their bacterial hosts. The abundance and Shannon diversity of ARGs on biodegradable poly hydroxy alkanoate (PHA) and non-biodegradable polyethylene terephthalate (PET) have no significant differences. Nevertheless, the abundance of multidrug resistance genes on PET (3.05 copies per 16S rRNA) was statistically higher than that on PHA (2.05). Beta diversity showed that the overall pattern of resistome on PHA was significantly distinct with that on PET. Procrustes analysis suggested a good-fit correlation between ARG profiles and bacterial community composition. The host-tracking analysis identified that Pseudomonas was always the major host for glycopeptide and multidrug resistance genes in PET and PHA biofilms, whereas the primary host for macrolide-lincosamide-streptogramin (MLS) changed to Desulfovibrio on PET. This study provided the first metagenomic insights into the ARGs and their hosts on biodegradable and non-biodegradable microplastics, suggesting that both two types of plastics harbor ARGs with preferences.},
}
@article {pmid33421868,
year = {2020},
author = {Chen, YH and Xue, F and Yu, SF and Li, XS and Liu, L and Jia, YY and Yan, WJ and Tan, QR and Wang, HN and Peng, ZW},
title = {Gut microbiota dysbiosis in depressed women: The association of symptom severity and microbiota function.},
journal = {Journal of affective disorders},
volume = {282},
number = {},
pages = {391-400},
doi = {10.1016/j.jad.2020.12.143},
pmid = {33421868},
issn = {1573-2517},
abstract = {BACKGROUND: The association between abnormal gut microbiome composition and depression is well established. However, the composition and functional capacity of the gut microbiota regarding depressed women has been poorly addressed.<br><br>METHODS: Stool samples from 62 female patients with major depressive disorder (MDD) and 46 healthy controls (Con) were analyzed by 16S rRNA gene sequencing; Twenty fecal samples from the patient group and 21 fecal samples from the Con group were further analyzed by shotgun metagenomic sequencing. Psychiatric symptoms and psychological, social, and professional functioning was also assessed.<br><br>RESULTS: Phylum Bacteroidetes, proteobaeteria, and Fusobacteria were greatly enriched in patients with MDD, while the Firmicutes and Actinobacteria phyla were consistently higher in Con. Notably, 18 microbial markers were identified on a random forest model and achieve an area under the curve of 0.92 between patients with MDD and the Con group. Forty-five species and their associated function were identified with statistically significant differences between patients with MDD and the Con group.<br><br>LIMITATIONS: The number of recruited samples, especially samples enrolled for shotgun metagenomic sequencing was relatively small, and the stool samples were collected only at baseline, making it difficult to establish a causal association between changes in gut microbiota compositions and disease remission.<br><br>CONCLUSIONS: This study characterizes the gut microbiota and their related function in female MDD. The gut microbiota-based biomarkers may be helpful in diagnosis and the altered gut microbial metabolites may contribute to the pathogenesis of MDD in women, representing potential microbial targets.},
}
@article {pmid33421848,
year = {2020},
author = {Wang, C and Hu, R and Strong, PJ and Zhuang, W and Huang, W and Luo, Z and Yan, Q and He, Z and Shu, L},
title = {Prevalence of antibiotic resistance genes and bacterial pathogens along the soil-mangrove root continuum.},
journal = {Journal of hazardous materials},
volume = {408},
number = {},
pages = {124985},
doi = {10.1016/j.jhazmat.2020.124985},
pmid = {33421848},
issn = {1873-3336},
abstract = {Plants roots are colonised by soil bacteria that are known to be the reservoir of antibiotic resistance genes (ARGs). ARGs can transfer between these microorganisms and pathogens, but to what extent these ARGs and pathogens disseminate from soil into plant is poorly understood. Here, we examined a high-resolution resistome profile along the soil-root continuum of mangrove saplings using amplicon and metagenomic sequencing. Data revealed that 91.4% of total ARGs were shared across four root-associated compartments (endosphere, episphere, rhizosphere and unplanted soil). Rather than compartment-selective dynamics of microbiota, the resistome was disseminated in a continuous fashion along the soil-root continuum. Such dissemination was independent of underlying root-associated bacterial and fungal microbiota, but might be facilitated by a multiplicity of mobile genetic elements. As the multiple-drug resistant pathogens, Vibrio vulnificus, pathogenic Escherichia coli and Klebsiella pneumoniae consistently predominated across four compartments, indicating the potential dissemination of antibiotic pathogens along the soil-root continuum. Through deciphering the profile and dynamics of the root-associated resistome and pathogens, our study identified the soil-root continuum as an interconnected sink through which certain ARGs and pathogens can flow from soil into the plant.},
}
@article {pmid33421714,
year = {2021},
author = {Liang, C and Wei, D and Zhang, S and Ren, Q and Shi, J and Liu, L},
title = {Removal of antibiotic resistance genes from swine wastewater by membrane filtration treatment.},
journal = {Ecotoxicology and environmental safety},
volume = {210},
number = {},
pages = {111885},
doi = {10.1016/j.ecoenv.2020.111885},
pmid = {33421714},
issn = {1090-2414},
abstract = {Antibiotic resistance genes (ARGs) have attracted extensive attention as an emerging environmental contaminant potentially threatening humans. One of the main emission sources of ARGs is swine wastewater. In this study, integrated membrane filtration including ultrafiltration and two-stage reverse osmosis was conducted for swine wastewater treatment. The abundances of 16 target ARGs, which accounted for 72.64% of the total ARGs in swine wastewater according to metagenomic sequencing, were quantified by quantitative real-time PCR (qPCR) during each stage of the membrane filtration process. The results showed that integrated membrane filtration could reduce more than 99.0% of conventional pollutants and 99.79% of ARGs (from 3.02 × 108 copy numbers/mL to 6.45 × 105 copy numbers/mL). Principal component analysis (PCA) indicated that the removal efficiency of ARGs subtype by membrane filtration did not depend on ARGs type. However, strong correlations were found between ARGs and the wastewater quality indicators TP, SS and EC according to Cooccurrence patterns, indicating that ARG removal was closely associated with insoluble solid particles and soluble ions in swine wastewater. These results showed that membrane filtration could not only remove conventional pollutants such as nitrogen and phosphorus but also reduce the emerging pollutant of ARGs and decrease the risk of ARGs flowing into natural water.},
}
@article {pmid33421499,
year = {2021},
author = {Verma, S and Meghwanshi, GK and Kumar, R},
title = {Current perspectives for microbial lipases from extremophiles and metagenomics.},
journal = {Biochimie},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biochi.2020.12.027},
pmid = {33421499},
issn = {1638-6183},
abstract = {Microbial lipases are most broadly used biocatalysts for environmental and industrial applications. Lipases catalyze the hydrolysis and synthesis of long acyl chain esters and have a characteristic folding pattern of α/β hydrolase with highly conserved catalytic triad (Serine, Aspartic/Glutamic acid and Histidine). Mesophilic lipases (optimal activity in neutral pH range, mesophilic temperature range, atmospheric pressure, normal salinity, non-radio-resistant, and instability in organic solvents) have been in use for many industrial biotransformation reactions. However, lipases from extremophiles can be used to design biotransformation reactions with higher yields, less byproducts or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. The extremophile lipase perform activity at extremes of temperature, pH, salinity, and pressure which can be screened from metagenome and de novo lipase design using computational approaches. Despite structural similarity, they exhibit great diversity at the sequence level. This diversity is broader when lipases from the bacterial, archaeal, plant, and animal domains/kingdoms are compared. Furthermore, a great diversity of novel lipases exists and can be discovered from the analysis of the dark matter - the unexplored nucleotide/metagenomic databases. This review is an update on extremophilic microbial lipases, their diversity, structure, and classification. An overview on novel lipases which have been detected through analysis of the genomic dark matter (metagenome) has also been presented.},
}
@article {pmid33420317,
year = {2021},
author = {Koeninger, L and Osbelt, L and Berscheid, A and Wendler, J and Berger, J and Hipp, K and Lesker, TR and Pils, MC and Malek, NP and Jensen, BAH and Brötz-Oesterhelt, H and Strowig, T and Jan Wehkamp, },
title = {Curbing gastrointestinal infections by defensin fragment modifications without harming commensal microbiota.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {47},
pmid = {33420317},
issn = {2399-3642},
abstract = {The occurrence and spread of multidrug-resistant pathogens, especially bacteria from the ESKAPE panel, increases the risk to succumb to untreatable infections. We developed a novel antimicrobial peptide, Pam-3, with antibacterial and antibiofilm properties to counter this threat. The peptide is based on an eight-amino acid carboxyl-terminal fragment of human β-defensin 1. Pam-3 exhibited prominent antimicrobial activity against multidrug-resistant ESKAPE pathogens and additionally eradicated already established biofilms in vitro, primarily by disrupting membrane integrity of its target cell. Importantly, prolonged exposure did not result in drug-resistance to Pam-3. In mouse models, Pam-3 selectively reduced acute intestinal Salmonella and established Citrobacter infections, without compromising the core microbiota, hence displaying an added benefit to traditional broad-spectrum antibiotics. In conclusion, our data support the development of defensin-derived antimicrobial agents as a novel approach to fight multidrug-resistant bacteria, where Pam-3 appears as a particularly promising microbiota-preserving candidate.},
}
@article {pmid33420281,
year = {2021},
author = {Wongsaroj, L and Chanabun, R and Tunsakul, N and Prombutara, P and Panha, S and Somboonna, N},
title = {First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {102},
pmid = {33420281},
issn = {2045-2322},
support = {GB-A 61 024 23 05//Thai Government Budget Grant/ ; },
abstract = {Northeastern Thailand relies on agriculture as a major economic activity, and has used high levels of agrochemicals due to low facility, and salty sandy soil. To support soil recovery and sustainable agriculture, local farmers have used organic fertilizers from farmed animal feces. However, knowledge about these animal fecal manures remains minimal restricting their optimal use. Specifically, while bacteria are important for soil and plant growth, an abundance and a diversity of bacterial composition in these animal fecal manures have not been reported to allow selection and adjustment for a more effective organic fertilizer. This study thereby utilized metagenomics combined with 16S rRNA gene quantitative PCR (qPCR) and sequencing to analyze quantitative microbiota profiles in association with nutrients (N, P, K), organic matters, and the other physiochemical properties, of the commonly used earthworm manure and other manures from livestock animals (including breed and feeding diet variations) in the region. Unlike the other manures, the earthworm manure demonstrated more favorable nutrient profiles and physiochemical properties for forming fertile soil. Despite low total microbial biomass, the microbiota were enriched with maximal OTUs and Chao richness, and no plant pathogenic bacteria were found based on the VFDB database. The microbial metabolic potentials supported functions to promote crop growth, such as C, N and P cyclings, xenobiotic degradation, and synthesis of bioactive compounds. Pearson's correlation analyses indicated that the quantitative microbiota of the earthworm manure were clustered in the same direction as N, and conductivity, salinity, and water content were essential to control the microbiota of animal manures.},
}
@article {pmid33420074,
year = {2021},
author = {Behary, J and Amorim, N and Jiang, XT and Raposo, A and Gong, L and McGovern, E and Ibrahim, R and Chu, F and Stephens, C and Jebeili, H and Fragomeli, V and Koay, YC and Jackson, M and O'Sullivan, J and Weltman, M and McCaughan, G and El-Omar, E and Zekry, A},
title = {Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {187},
pmid = {33420074},
issn = {2041-1723},
abstract = {The gut microbiota is reported to modulate the immune response in hepatocellular carcinoma (HCC). Here, we employ metagenomic and metabolomic studies to characterise gut microbiota in patients with non-alcoholic fatty liver disease (NAFLD) related cirrhosis, with or without HCC, and evaluate its effect on the peripheral immune response in an ex vivo model. We find that dysbiosis characterises the microbiota of patients with NAFLD-cirrhosis, with compositional and functional shifts occurring with HCC development. Gene function of the microbiota in NAFLD-HCC supports short chain fatty acid production, and this is confirmed by metabolomic studies. Ex vivo studies show that bacterial extracts from the NAFLD-HCC microbiota, but not from the control groups, elicit a T cell immunosuppressive phenotype, characterised by expansion of regulatory T cells and attenuation of CD8 + T cells. Our study suggest that the gut microbiota in NAFLD-HCC is characterised by a distinctive microbiome/metabolomic profile, and can modulate the peripheral immune response.},
}
@article {pmid33419189,
year = {2021},
author = {Bellassi, P and Rocchetti, G and Nocetti, M and Lucini, L and Masoero, F and Morelli, L},
title = {A Combined Metabolomic and Metagenomic Approach to Discriminate Raw Milk for the Production of Hard Cheese.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {1},
pages = {},
doi = {10.3390/foods10010109},
pmid = {33419189},
issn = {2304-8158},
abstract = {The chemical composition of milk can be significantly affected by different factors across the dairy supply chain, including primary production practices. Among the latter, the feeding system could drive the nutritional value and technological properties of milk and dairy products. Therefore, in this work, a combined foodomics approach based on both untargeted metabolomics and metagenomics was used to shed light onto the impact of feeding systems (i.e., hay vs. a mixed ration based on hay and fresh forage) on the chemical profile of raw milk for the production of hard cheese. In particular, ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-QTOF) was used to investigate the chemical profile of raw milk (n = 46) collected from dairy herds located in the Po River Valley (Italy) and considering different feeding systems. Overall, a total of 3320 molecular features were putatively annotated across samples, corresponding to 734 unique compound structures, with significant differences (p < 0.05) between the two feeding regimens under investigation. Additionally, supervised multivariate statistics following metabolomics-based analysis allowed us to clearly discriminate raw milk samples according to the feeding systems, also extrapolating the most discriminant metabolites. Interestingly, 10 compounds were able to strongly explain the differences as imposed by the addition of forage in the cows' diet, being mainly glycerophospholipids (i.e., lysophosphatidylethanolamines, lysophosphatidylcholines, and phosphatidylcholines), followed by 5-(3',4'-Dihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide, 5a-androstan-3a,17b-diol disulfuric acid, and N-stearoyl glycine. The markers identified included both feed-derived (such as phenolic metabolites) and animal-derived compounds (such as lipids and derivatives). Finally, although characterized by a lower prediction ability, the metagenomic profile was found to be significantly correlated to some milk metabolites, with Staphylococcaceae, Pseudomonadaceae, and Dermabacteraceae establishing a higher number of significant correlations with the discriminant metabolites. Therefore, taken together, our preliminary results provide a comprehensive foodomic picture of raw milk samples from different feeding regimens, thus supporting further ad hoc studies investigating the metabolomic and metagenomic changes of milk in all processing conditions.},
}
@article {pmid33418927,
year = {2021},
author = {Govil, T and Paste, M and Samanta, D and David, A and Goh, KM and Li, X and Salem, DR and Sani, RK},
title = {Metagenomics and Culture Dependent Insights into the Distribution of Firmicutes across Two Different Sample Types Located in the Black Hills Region of South Dakota, USA.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/microorganisms9010113},
pmid = {33418927},
issn = {2076-2607},
support = {1736255//National Science Foundation/ ; 1849206//National Science Foundation/ ; 1920954//National Science Foundation/ ; },
abstract = {Firmicutes is almost a ubiquitous phylum. Several genera of this group, for instance, Geobacillus, are recognized for decomposing plant organic matter and for producing thermostable ligninolytic enzymes. Amplicon sequencing was used in this study to determine the prevalence and genetic diversity of the Firmicutes in two distinctly related environmental samples-South Dakota Landfill Compost (SDLC, 60 °C), and Sanford Underground Research Facility sediments (SURF, 45 °C). Although distinct microbial community compositions were observed, there was a dominance of Firmicutes in both the SDLC and SURF samples, followed by Proteobacteria. The abundant classes of bacteria in the SDLC site, within the phylum Firmicutes, were Bacilli (83.2%), and Clostridia (2.9%). In comparison, the sample from the SURF mine was dominated by the Clostridia (45.8%) and then Bacilli (20.1%). Within the class Bacilli, the SDLC sample had more diversity (a total of 11 genera with more than 1% operational taxonomic unit, OTU). On the other hand, SURF samples had just three genera, about 1% of the total population: Bacilli, Paenibacillus, and Solibacillus. With specific regard to Geobacillus, it was found to be present at a level of 0.07% and 2.5% in SURF and SDLC, respectively. Subsequently, culture isolations of endospore-forming Firmicutes members from these samples led to the isolation of a total of 117 isolates. According to colony morphologies, and identification based upon 16S rRNA and gyrB gene sequence analysis, we obtained 58 taxonomically distinct strains. Depending on the similarity indexes, a gyrB sequence comparison appeared more useful than 16S rRNA sequence analysis for inferring intra- and some intergeneric relationships between the isolates.},
}
@article {pmid33418922,
year = {2021},
author = {Zhang, Z and Liu, D and Wang, D and Wu, Q},
title = {Library Preparation Based on Transposase Assisted RNA/DNA Hybrid Co-Tagmentation for Next-Generation Sequencing of Human Noroviruses.},
journal = {Viruses},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/v13010065},
pmid = {33418922},
issn = {1999-4915},
support = {31772078//National Natural Science Foundation of China/ ; },
abstract = {Human noroviruses (HuNoVs) are one of the leading causes of foodborne illnesses globally. The viral genome is the most essential information for viral source tracing and viral transmission pattern monitoring. However, whole genome sequencing of HuNoVs is still challenging due to the sequence heterogeneity among different genotypes and low titer in samples. To address this need, in this study, the Transposase assisted RNA/DNA hybrid Co-tagmentation (TRACE-seq) method was established for next generation sequencing library preparation of HuNoVs. Our data demonstrated that almost the whole HuNoVs genome (>7 kb) could be obtained from all of the 11 clinical samples tested. Twelve genotypes including GI.3, GI.4, GI.5, GI.8, GII.2, GII.3, GII.4, GII.6, GII.12, GII.13, GII.14, and GII.21 were involved. Compared with the traditional method for viral metagenomics library preparation, optimized TRACE-seq greatly reduced the interference from the host's and bacterial RNAs. In addition, viral genome sequences can be assembled by using less raw data with sufficient depth along the whole genome. Therefore, for the high versatility and reliability, this method is promising for whole viral genome attainment. It is particularly applicable for the viruses with a low titer that are mixed with a complicated host background and are unable to be cultured in vitro, like the HuNoVs utilized in this study.},
}
@article {pmid33418661,
year = {2018},
author = {Tao, LY and Gong, JS and Su, C and Jiang, M and Li, H and Li, H and Lu, ZM and Xu, ZH and Shi, JS},
title = {Mining and Expression of a Metagenome-Derived Keratinase Responsible for Biosynthesis of Silver Nanoparticles.},
journal = {ACS biomaterials science &amp; engineering},
volume = {4},
number = {4},
pages = {1307-1315},
doi = {10.1021/acsbiomaterials.7b00687},
pmid = {33418661},
issn = {2373-9878},
abstract = {A keratinase gene kerBv was mined from soil metagenomes. The open reading frame consisted of 1149 bp and potentially encoded a protein of 382 amino acid residues. It shared the same active site with several reported typical keratinases via analysis of the amino acid sequence. The keratinase was successfully expressed in B. subtilis WB600 with pMA5 expression vector. The maximum activity of 164.8 U/mL in the fermentation supernatant was observed after incubating for 30 h in Terrifc Broth (TB) medium. The keratinase exhibited outstanding resistance to metal ions and was surfactant-stable. Additionally, the enzyme displayed broad substrate specificity especially toward insoluble substrate feather meal because of its disulfide bond-reducing activity. Furthermore, the reducing power of the recombinant keratinase was investigated. It showed that the protein exhibited a relatively high reducing power, which was subsequently used in the biosynthesis of silver nanoparticles (AgNPs). The biosynthesized AgNPs were characterized by ultraviolet-visible (UV-vis) spectroscopy, dynamic light scattering (DLS), transmission electron microscope (TEM), as well as Fourier transform infrared spectroscopy (FTIR) and displayed obvious antibacterial activities toward Escherichia coli.},
}
@article {pmid33418085,
year = {2021},
author = {Yao, G and Zhang, W and Yang, M and Yang, H and Wang, J and Zhang, H and Wei, L and Xie, Z and Li, W},
title = {MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.gpb.2020.11.001},
pmid = {33418085},
issn = {2210-3244},
abstract = {Microbes play important roles in human health and disease. The interaction between microbes and hosts is a reciprocal relationship, which remains largely under-explored. Current computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We developed the MicroPhenoDB database by manually curating and consistently integrating microbe-disease association data. MicroPhenoDB provides 5677 non-redundant associations between 1781 microbes and 542 human disease phenotypes across more than 22 human body sites. MicroPhenoDB also provides 696,934 relationships between 27,277 unique clade-specific core genes and 685 microbes. Disease phenotypes are classified and described using the Experimental Factor Ontology (EFO). A refined score model was developed to prioritize the associations based on evidential metrics. The sequence search option in MicroPhenoDB enables rapid identification of existing pathogenic microbes in samples without running the usual metagenomic data processing and assembly. MicroPhenoDB offers data browsing, searching, and visualization through user-friendly web interfaces and web service application programming interfaces. MicroPhenoDB is the first database platform to detail the relationships between pathogenic microbes, core genes, and disease phenotypes. It will accelerate metagenomic data analysis and assist studies in decoding microbes related to human diseases. MicroPhenoDB is available through http://www.liwzlab.cn/microphenodb and http://lilab2.sysu.edu.cn/microphenodb.},
}
@article {pmid33417825,
year = {2021},
author = {Scharf, ME and Peterson, BF},
title = {A Century of Synergy in Termite Symbiosis Research: Linking the Past with New Genomic Insights.},
journal = {Annual review of entomology},
volume = {66},
number = {},
pages = {23-43},
doi = {10.1146/annurev-ento-022420-074746},
pmid = {33417825},
issn = {1545-4487},
abstract = {Termites have long been studied for their symbiotic associations with gut microbes. In the late nineteenth century, this relationship was poorly understood and captured the interest of parasitologists such as Joseph Leidy; this research led to that of twentieth-century biologists and entomologists including Cleveland, Hungate, Trager, and Lüscher. Early insights came via microscopy, organismal, and defaunation studies, which led to descriptions of microbes present, descriptions of the roles of symbionts in lignocellulose digestion, and early insights into energy gas utilization by the host termite. Focus then progressed to culture-dependent microbiology and biochemical studies of host-symbiont complementarity, which revealed specific microhabitat requirements for symbionts and noncellulosic mechanisms of symbiosis (e.g., N2 fixation). Today, knowledge on termite symbiosis has accrued exponentially thanks to omic technologies that reveal symbiont identities, functions, and interdependence, as well as intricacies of host-symbiont complementarity. Moving forward, the merging of classical twentieth-century approaches with evolving omic tools should provide even deeper insights into host-symbiont interplay.},
}
@article {pmid33416984,
year = {2021},
author = {Busch, P and Suleiman, M and Schäfers, C and Antranikian, G},
title = {A multi-omic screening approach for the discovery of thermoactive glycoside hydrolases.},
journal = {Extremophiles : life under extreme conditions},
volume = {},
number = {},
pages = {},
pmid = {33416984},
issn = {1433-4909},
abstract = {Next-generation sequencing and computational biology have facilitated the implementation of new combinatorial screening approaches to discover novel enzymes of biotechnological interest. In this study, we describe the successful establishment of a multi-omic approach for the identification of thermostable hydrolase-encoding genes by determination of gene expression levels. We applied this combinatorial approach using an anaerobic enrichment culture from an Azorean hot spring sample grown on green coffee beans as recalcitrant substrate. An in-depth analysis of the microbial community resulted in microorganisms capable of metabolizing the selected substrate, such as the genera Caloramator, Dictyoglomus and Thermoanaerobacter as active and abundant microorganisms. To discover glycoside hydrolases, 90,342 annotated genes were screened for specific reaction types. A total number of 106 genes encoding cellulases (EC 3.2.1.4), beta-glucosidases (EC 3.2.1.21) and endo-1,4-beta-mannosidases (EC 3.2.1.78) were selected. Mapping of RNA-Seq reads to the related metagenome led to expression levels for each gene. Amongst those, 14 genes, encoding glycoside hydrolases, showed highest expression values, and were used for further cloning. Four proteins were biochemically characterized and were identified as thermoactive glycoside hydrolases with a broad substrate range. This work demonstrated that a combinatory omic approach is a suitable strategy identifying unique thermoactive enzymes from environmental samples.},
}
@article {pmid33414773,
year = {2020},
author = {Lu, Z and Xu, Z and Kong, L and Shen, H and Aschenbach, JR},
title = {Functional Changes of the Community of Microbes With Ni-Dependent Enzyme Genes Accompany Adaptation of the Ruminal Microbiome to Urea-Supplemented Diets.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {596681},
doi = {10.3389/fmicb.2020.596681},
pmid = {33414773},
issn = {1664-302X},
abstract = {Urea is an inexpensive non-protein nitrogen source commonly supplemented to the diets of ruminants. It is cleaved to ammonia by bacterial ureases, which require Ni as a catalyst for ureolysis. The key event in the changes of the ruminal microbiome after urea supplementation remains unknown. We have therefore investigated changes in the ruminal microbiome and its community with Ni-dependent enzyme genes following urea supplementation and analyzed the associations of rumen environmental factors, including fermentation variables and Ni concentrations, with the compositional and functional changes of these communities. We found that urea supplementation increased urease activity and the concentrations of ammonia and Ni, and tended to increase concentrations of short chain fatty acids and acetate, whereas it decreased rumen pH and the L-/D-lactate ratio. With standards for genome completeness >60% and strain heterogeneity <10%, 20 bacterial species containing five Ni-dependent enzyme genes were detected in the metagenome sequences. For the five Ni-dependent enzyme genes, urea supplementation increased the relative abundances of genes of urease and acetyl-CoA synthase, whereas it decreased the relative abundances of genes of glyoxalase I, [NiFe]-hydrogenase, and lactate racemase. For the 20 microbes with Ni-dependent enzyme genes, urea supplementation increased the relative abundances of five bacteria exhibiting high capacities for the utilization of hemicellulose and pectin for butyrate and fatty acid biosynthesis. For the ruminal microbiome, urea supplementation increased the metagenomic capacities for hemicellulose and pectin degradation, butyrate generation, fatty acid biosynthesis, and carbon fixation, whereas it decreased the metagenomic capacities for starch degradation, propionate generation, and sulfur and nitrogen metabolism. Constrained correspondence analysis identified rumen ammonia and Ni concentrations as likely driving factors in the reshaping of the ruminal microbiome and, together with pH, of the community of microbes with Ni-dependent enzyme genes. Thus, the functional change of the latter community is probably an important event in the adaptation of the ruminal microbiome to urea-supplemented diets. This result provides a new perspective for the understanding of the effects of urea supplementation on rumen fermentation.},
}
@article {pmid33414326,
year = {2021},
author = {Amanbayeva, M and Anarkulova, E and Bogoyavlenskiy, A and Alexyuk, M and Imangazy, A and Berezin, V},
title = {Metagenomic Exploration of Atelerix albiventris Gut Microbiome.},
journal = {Microbiology resource announcements},
volume = {10},
number = {1},
pages = {},
pmid = {33414326},
issn = {2576-098X},
abstract = {Here, we report the metagenomic analysis of the gut of Atelerix albiventris, an animal typically kept as a pet in Kazakhstan. In this case, shotgun metagenomic sequencing of the RNA and DNA viral community was performed.},
}
@article {pmid33414318,
year = {2021},
author = {Babalola, OO and Omotayo, OP and Igiehon, NO},
title = {Survey of Maize Rhizosphere Microbiome Using Shotgun Metagenomics.},
journal = {Microbiology resource announcements},
volume = {10},
number = {1},
pages = {},
pmid = {33414318},
issn = {2576-098X},
abstract = {Several processes which occur in the rhizosphere make it a vital region in plant development. However, studies that examine rhizosphere microbiomes and their functional potentials remain scarce. Shotgun metagenomics was employed here to evaluate the functional potentials of the maize rhizosphere microbiome of farms in two South African provinces.},
}
@article {pmid33413361,
year = {2021},
author = {Ye, X and Zhou, L and Zhang, Y and Xue, S and Gan, QF and Fang, S},
title = {Effect of host breeds on gut microbiome and serum metabolome in meat rabbits.},
journal = {BMC veterinary research},
volume = {17},
number = {1},
pages = {24},
pmid = {33413361},
issn = {1746-6148},
abstract = {BACKGROUND: Gut microbial compositional and functional variation can affect health and production performance of farm animals. Analysing metabolites in biological samples provides information on the basic mechanisms that affect the well-being and production traits in farm animals. However, the extent to which host breeds affect the gut microbiome and serum metabolome in meat rabbits is still unknown. In this study, the differences in phylogenetic composition and functional capacities of gut microbiota in two commercial rabbit breeds Elco and Ira were determined by 16S rRNA gene and metagenomic sequencing. The alternations in serum metabolome in the two rabbit breeds were detected using ultra-performance liquid chromatography system coupled with quadrupole time of flight mass spectrometry (UPLC-QTOFMS).<br><br>RESULTS: Sequencing results revealed that there were significant differences in the gut microbiota of the two breeds studied, suggesting that host breeds affect structure and diversity of gut microbiota. Numerous breed-associated microorganisms were identified at different taxonomic levels and most microbial taxa belonged to the families Lachnospiraceae and Ruminococcaceae. In particular, several short-chain fatty acids (SCFAs) producing species including Coprococcus comes, Ruminococcus faecis, Ruminococcus callidus, and Lachnospiraceae bacterium NK4A136 could be considered as biomarkers for improving the health and production performance in meat rabbits. Additionally, gut microbial functional capacities related to bacterial chemotaxis, ABC transporters, and metabolism of different carbohydrates, amino acids, and lipids varied greatly between rabbit breeds. Several fatty acids, amino acids, and organic acids in the serum were identified as breed-associated, where certain metabolites could be regarded as biomarkers correlated with the well-being and production traits of meat rabbits. Correlation analysis between breed-associated microbial species and serum metabolites revealed significant co-variations, indicating the existence of cross-talk among host-gut microbiome-serum metabolome.<br><br>CONCLUSIONS: Our study provides insight into how gut microbiome and serum metabolome of meat rabbits are affected by host breeds and uncovers potential biomarkers important for breed improvement of meat rabbits.},
}
@article {pmid33413128,
year = {2021},
author = {Mustafa, GR and Li, C and Zhao, S and Jin, L and He, X and Shabbir, MZ and He, Y and Li, T and Deng, W and Xu, L and Xiong, Y and Zhang, G and Zhang, H and Huang, Y and Zou, L},
title = {Metagenomic analysis revealed a wide distribution of antibiotic resistance genes and biosynthesis of antibiotics in the gut of giant pandas.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {15},
pmid = {33413128},
issn = {1471-2180},
support = {KLSFGAGP2020.003//Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park (CCRCGP)/ ; No. 2017115//State Forestry Administration/ ; GH201709//International Cooperation project of giant panda/ ; },
abstract = {BACKGROUND: The gut microbiome is essential for the host's health and serves as an essential reservoir of antibiotic resistance genes (ARGs). We investigated the effects of different factors, including the dietary shifts and age, on the functional characteristics of the giant panda's gut microbiome (GPs) through shotgun metagenome sequencing. We explored the association between gut bacterial genera and ARGs within the gut based on network analysis.<br><br>RESULTS: Fecal samples (n=60) from captive juvenile, adult, and geriatric GPs were processed, and variations were identified in the gut microbiome according to different ages, the abundance of novel ARGs and the biosynthesis of antibiotics. Among 667 ARGs identified, nine from the top ten ARGs had a higher abundance in juveniles. For 102 ARGs against bacteria, a co-occurrence pattern revealed a positive association for predominant ARGs with Streptococcus. A comparative KEGG pathways analysis revealed an abundant biosynthesis of antibiotics among three different groups of GPs, where it was more significantly observed in the juvenile group. A co-occurrence pattern further revealed a positive association for the top ten ARGs, biosynthesis of antibiotics, and metabolic pathways.<br><br>CONCLUSION: Gut of GPs serve as a reservoir for novel ARGs and biosynthesis of antibiotics. Dietary changes and age may influence the gut microbiome's functional characteristics; however, it needs further studies to ascertain the study outcomes.},
}
@article {pmid32156318,
year = {2020},
author = {Macey, MC and Pratscher, J and Crombie, AT and Murrell, JC},
title = {Impact of plants on the diversity and activity of methylotrophs in soil.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {31},
doi = {10.1186/s40168-020-00801-4},
pmid = {32156318},
issn = {2049-2618},
mesh = {Alcohol Oxidoreductases/genetics ; Bacteria/*classification/metabolism ; DNA, Bacterial/genetics ; *Genetic Variation ; Metagenome ; Methanol/*metabolism ; Methylobacterium/classification/metabolism ; Phylogeny ; *Plant Physiological Phenomena ; Plants/metabolism ; RNA, Ribosomal, 16S/metabolism ; Rhizosphere ; *Soil Microbiology ; },
abstract = {BACKGROUND: Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils.<br><br>RESULTS: Application of probes for methanol dehydrogenase genes (mxaF, xoxF, mdh2) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including Hyphomicrobium, Methylobacterium and members of the Comamonadaceae. The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using 13C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the 13C-labelled DNA revealed members of the Methylophilaceae as highly abundant and active in all soils examined. There was greater diversity of active members of the Methylophilaceae and Comamonadaceae and of the genus Methylobacterium in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a 13CO2 atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere.<br><br>CONCLUSION: In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle. Video abstract.},
}
@article {pmid33411719,
year = {2021},
author = {Elmassry, MM and Kim, S and Busby, B},
title = {Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0244876},
doi = {10.1371/journal.pone.0244876},
pmid = {33411719},
issn = {1932-6203},
abstract = {Characterizing the gut microbiota in terms of their capacity to interfere with drug metabolism is necessary to achieve drug efficacy and safety. Although examples of drug-microbiome interactions are well-documented, little has been reported about a computational pipeline for systematically identifying and characterizing bacterial enzymes that process particular classes of drugs. The goal of our study is to develop a computational approach that compiles drugs whose metabolism may be influenced by a particular class of microbial enzymes and that quantifies the variability in the collective level of those enzymes among individuals. The present paper describes this approach, with microbial β-glucuronidases as an example, which break down drug-glucuronide conjugates and reactivate the drugs or their metabolites. We identified 100 medications that may be metabolized by β-glucuronidases from the gut microbiome. These medications included morphine, estrogen, ibuprofen, midazolam, and their structural analogues. The analysis of metagenomic data available through the Sequence Read Archive (SRA) showed that the level of β-glucuronidase in the gut metagenomes was higher in males than in females, which provides a potential explanation for the sex-based differences in efficacy and toxicity for several drugs, reported in previous studies. Our analysis also showed that infant gut metagenomes at birth and 12 months of age have higher levels of β-glucuronidase than the metagenomes of their mothers and the implication of this observed variability was discussed in the context of breastfeeding as well as infant hyperbilirubinemia. Overall, despite important limitations discussed in this paper, our analysis provided useful insights on the role of the human gut metagenome in the variability in drug response among individuals. Importantly, this approach exploits drug and metagenome data available in public databases as well as open-source cheminformatics and bioinformatics tools to predict drug-metagenome interactions.},
}
@article {pmid33411134,
year = {2021},
author = {Barzkar, N and Sohail, M and Tamadoni Jahromi, S and Gozari, M and Poormozaffar, S and Nahavandi, R and Hafezieh, M},
title = {Marine Bacterial Esterases: Emerging Biocatalysts for Industrial Applications.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {33411134},
issn = {1559-0291},
abstract = {The marine ecosystem has been known to be a significant source of novel enzymes. Esterase enzymes (EC 3.1.1.1) represent a diverse group of hydrolases that catalyze the cleavage and formation of ester bonds. Although esterases are widely distributed among marine organisms, only microbial esterases are of paramount industrial importance. This article discusses the importance of marine microbial esterases, their biochemical and kinetic properties, and their stability under extreme conditions. Since culture-dependent techniques provide limited insights into microbial diversity of the marine ecosystem, therefore, genomics and metagenomics approaches have widely been adopted in search of novel esterases. Additionally, the article also explains industrial applications of marine bacterial esterases particularly for the synthesis of optically pure substances, the preparation of enantiomerically pure drugs, the degradation of human-made plastics and organophosphorus compounds, degradation of the lipophilic components of the ink, and production of short-chain flavor esters.},
}
@article {pmid33410957,
year = {2021},
author = {Chang, H and Mishra, R and Cen, C and Tang, Y and Ma, C and Wasti, S and Wang, Y and Ou, Q and Chen, K and Zhang, J},
title = {Metagenomic Analyses Expand Bacterial and Functional Profiling Biomarkers for Colorectal Cancer in a Hainan Cohort, China.},
journal = {Current microbiology},
volume = {},
number = {},
pages = {},
pmid = {33410957},
issn = {1432-0991},
support = {ZDYF2019150//Key Research and Development Project of Hainan Province (CN)/ ; },
abstract = {This study was conducted for the metagenomic analysis of stool samples from CRC affected individuals to identify biomarkers for CRC in Hainan, the only tropical island province of China. The gut microbiota of CRC patients differed significantly from that of healthy and reference database cohorts based on Aitchison distance and Bray-Cutis distance but there was no significant difference in alpha diversity. Furthermore, at the species level, 68 species were significantly altered including 37 CRC-enriched, such as, Fusobacterium nucleatum, Parvimonas micra, Gemella morbillorum, Citrobacter portucalensis, Alloprevotella sp., Shigella sonnei, Coriobacteriaceae bacterium, etc. Sixty-seven different metabolic pathways were acquired, and pathways involved in the synthesis of many amino acids were significantly declined. Besides, 2 identified antibiotic resistance genes performed well (area under the receive-operation curve AUC = 0.833, 95% CI 58.51-100%) compared with virulence factor genes. The results of the present study provide region-specific bacterial and functional biomarkers of gut microbiota for CRC patients in Hainan. Microbiota is considered as a non-invasive biomarker for the detection of CRC. Gut microbiota of different geographic regions should be further studied to expand the understanding of markers, especially for the China cohort due to diverse nationalities and lifestyles.},
}
@article {pmid33410936,
year = {2021},
author = {St James, AR and Lin, J and Richardson, RE},
title = {Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {33410936},
issn = {1432-184X},
abstract = {Peatland microbial community composition varies with respect to a range of biological and physicochemical variables. While the extent of peat degradation (humification) has been linked to microbial community composition along vertical stratification gradients within peatland sites, across-site variations have been relatively unexplored. In this study, we compared microbial communities across ten pristine Sphagnum-containing peatlands in the Adirondack Mountains, NY, which represented three different peat types-humic fen peat, humic bog peat, and fibric bog peat. Using 16S amplicon sequencing and network correlation analysis, we demonstrate that microbial community composition is primarily linked to peat type, and that distinct taxa networks distinguish microbial communities in each type. Shotgun metagenomic sequencing of the active water table region (mesotelm) from two Sphagnum-dominated bogs-one with fibric peat and one with humic peat-revealed differences in primary carbon degradation pathways, with the fibric peat being dominated by carbohydrate metabolism and hydrogenotrophic methanogenesis, and the humic peat being dominated by aliphatic carbon metabolism and aceticlastic methanogenesis. Our results suggest that peat humification is a major factor driving microbial community dynamics across peatland ecosystems.},
}
@article {pmid33410935,
year = {2021},
author = {Li, W and Nelson, KE},
title = {Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {33410935},
issn = {1432-184X},
abstract = {In recent years, many studies have described the composition and function of the human microbiome at different body sites and suggested a role for the microbiome in various diseases and health conditions. Some studies, using longitudinal samples, have also suggested how the microbiome changes over time due to disease, diet, development, travel, and other environmental factors. However, to date, no study has demonstrated whether the microorganisms established at birth or in early childhood, either transmitted from parents or obtained from the environment, can stay in the human body until adult or senior age. To directly answer this question is difficult, because microbiome samples at childhood and at later adulthood for the same individual will need to be compared and the field is not old enough to have allowed for that type of sample collection. Here, using a metagenomic approach, we analyzed 1004 gut microbiome samples from senior adults (65 ± 7.8 years) from the TwinsUK cohort. Our data indicate that many species in the human gut acquired in early childhood can stay for a lifetime until senior ages. We identified the rare genomic variants (single nucleotide variation and indels) for 27 prevalent species with enough sequencing coverage for confident genomic variant identification. We found that for some species, twin pairs, including both monozygotic (MZ) and dizygotic (DZ) twins, share significantly more rare variants than unrelated subject pairs. But no significant difference is found between MZ and DZ twin pairs. These observations strongly suggest that these species acquired in early childhood remained in these persons until senior adulthood.},
}
@article {pmid33410932,
year = {2021},
author = {Hutchinson, MI and Bell, TAS and Gallegos-Graves, V and Dunbar, J and Albright, M},
title = {Merging Fungal and Bacterial Community Profiles via an Internal Control.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {33410932},
issn = {1432-184X},
support = {F255LANL2018//Office of Science/ ; },
abstract = {Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. This IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.},
}
@article {pmid33410931,
year = {2021},
author = {Gomez, JA and Primm, TP},
title = {A Slimy Business: the Future of Fish Skin Microbiome Studies.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {33410931},
issn = {1432-184X},
abstract = {Fish skin contains a mucosal microbiome for the largest and oldest group of vertebrates, a location ideal for microbial community ecology and practical applications in agriculture and veterinary medicine. These selective microbiomes are dominated by Proteobacteria, with compositions different from the surrounding water. Core taxa are a small percentage of those present and are currently functionally uncharacterized. Methods for skin sampling, DNA extraction and amplification, and sequence data processing are highly varied across the field, and reanalysis of recent studies using a consistent pipeline revealed that some conclusions did change in statistical significance. Further, the 16S gene sequencing approaches lack quantitation of microbes and copy number adjustment. Thus, consistency in the field is a serious limitation in comparing across studies. The most significant area for future study, requiring metagenomic and metabolomics data, is the biochemical pathways and functions within the microbiome community, the interactions between members, and the resulting effects on fish host health being linked to specific nutrients and microbial species. Genes linked to skin colonization, such as those for attachment or mucin degradation, need to be uncovered and explored. Skin immunity factors need to be directly linked to microbiome composition and individual taxa. The basic foundation has been laid, and many exciting future discoveries remain.},
}
@article {pmid33410648,
year = {2020},
author = {To, RK and Ramchandar, N and Gupta, A and Pong, A and Cannavino, C and Foley, J and Farnaes, L and Coufal, NG},
title = {Use of Plasma Metagenomic Next-generation Sequencing for Pathogen Identification in Pediatric Endocarditis.},
journal = {The Pediatric infectious disease journal},
volume = {Publish Ahead of Print},
number = {},
pages = {},
doi = {10.1097/INF.0000000000003038},
pmid = {33410648},
issn = {1532-0987},
abstract = {Pediatric infective endocarditis incurs significant morbidity and generally occurs among children with underlying heart disease. Identification of a pathogen is critical in determining appropriate therapy. However, standard diagnostic testing has limited sensitivity. We describe a case series of children with infective endocarditis in whom plasma next-generation sequencing (Karius, Redwood, CA) identified an organism in 8 of 10 cases.},
}
@article {pmid33410624,
year = {2021},
author = {Xu, SF and Tian, Q and Tian, YL and Feng, J and Zhao, J and Yin, XB},
title = {Detection of infectious pathogens located in the peripheral lung field by metagenomic next-generation sequencing combined with virtual bronchoscopic navigation.},
journal = {Chinese medical journal},
volume = {Publish Ahead of Print},
number = {},
pages = {},
doi = {10.1097/CM9.0000000000001339},
pmid = {33410624},
issn = {2542-5641},
}
@article {pmid33410172,
year = {2021},
author = {Ng, E and Tay, JRH and Balan, P and Ong, MMA and Bostanci, N and Belibasakis, GN and Seneviratne, CJ},
title = {Metagenomic sequencing provides new insights into the subgingival bacteriome and aetiopathology of periodontitis.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.12811},
pmid = {33410172},
issn = {1600-0765},
support = {//National Dental Research Institute Singapore/ ; },
abstract = {&quot;Open-ended&quot; molecular techniques such as 16S rRNA sequencing have revealed that the oral bacteriome of subgingival plaque is more diverse than originally thought. 16S rRNA analysis has demonstrated that constituents of the overall bacterial community are qualitatively similar in health and disease, differing mainly in their relative proportions with respect to each other. Species in low abundance can also act as critical species, leading to the concept of global community dysbiosis which relates to shifts in community structure, rather than shifts in membership. Correlation analysis suggests that coordinated interactions in the community are essential for incipient dysbiosis and disease pathogenesis. The subgingival bacteriome also provides biomarkers that are useful for disease detection and management. Combined with clinical and biological parameters, these may assist clinicians in developing and implementing effective treatment strategies to restore microbial homeostasis and monitor disease. Identification of higher risk groups or poor responders to treatment using unique subgingival bacteriome signatures may also lead to early intervention.},
}
@article {pmid33410140,
year = {2021},
author = {Joshi, N and Kaushal, G and Singh, SP},
title = {Biochemical characterization of a novel thermo-halo-tolerant GH5 endoglucanase from a thermal spring metagenome.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.27668},
pmid = {33410140},
issn = {1097-0290},
abstract = {A novel endoglucanase gene, celM , was cloned from a thermal spring metagenome. The gene was expressed in Escherichia coli, and the protein was extracted and purified. The protein catalysed the hydrolysis of amorphous cellulose in a wide range of temperature, 30°C to 95°C, with optimal activity at 80°C. It was able to tolerate high temperature (80°C) with a half-life of 8 h. Its activity was eminent in a wide pH range of 3.0 to 11.0, with the highest activity at pH 6.0. The enzyme was tested for halostability. Any significant loss was not recorded in the activity of CelM after the exposure to salinity (3M NaCl) for 30 days. Furthermore, CelM displayed substantial resistance towards metal ions, denaturant, reducing agent, organic solvent, and non-ionic surfactants. The amorphous cellulose, treated with CelM , was randomly cleaved, generating cellooligosaccharides of 2 to 5 degree of polymerization. Furthermore, CelM was demonstrated to catalyse the hydrolysis of cellulose fraction in the delignified biomass samples, e.g., sweet sorghum bagasse, rice straw, and corncob, into cello-oligosaccharides. Given that CelM is a thermo-halo-tolerant GH5 endoglucanase, with resistance to detergents and organic solvent, the biocatalyst could be of potential usefulness for a variety of industrial applications. This article is protected by copyright. All rights reserved.},
}
@article {pmid33410044,
year = {2021},
author = {Lyu, Y and Yang, T and Liu, H and Qi, Z and Li, P and Shi, Z and Xiang, Z and Gong, D and Li, N and Zhang, Y},
title = {Enrichment and characterization of an effective hexavalent chromium-reducing microbial community YEM001.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {33410044},
issn = {1614-7499},
support = {2019ABA114//Major Project for Special Technology Innovation of Hubei Province/ ; 2017ABA157//Major Project for Special Technology Innovation of Hubei Province/ ; 31370506//National Natural Science Foundation of China/ ; 21776162//National Natural Science Foundation of China/ ; 31500422//National Natural Science Foundation of China/ ; },
abstract = {Chromium (Cr) is one of the most widely used heavy metals in industrial processes, resulting in water and soil pollution that seriously threaten environmental safety. In this paper, we have directionally enriched a Cr(VI)-reducing bacterial community YEM001 from no-Cr(VI) polluted pond sedimental sludge by selectively growing it in Cr(VI)-containing media. This community could effectively reduce Cr(VI) in laboratory rich media containing different concentrations of Cr(VI), such as 61% reduction at 435 mg/L Cr(VI), 85% reduction at 355 mg/L Cr(VI), and complete reduction at 269 mg/L Cr(VI) in 93.5 h. It was also able to completely reduce 100 mg/L and 300 mg/L Cr(VI) in landfill leachate and natural sludge in 48 h, respectively. Optimal pH for Cr(VI) reduction of the YEM001 is between 7 and 8 and the best efficiency for Cr(VI) reduction occurs at 30 °C. Metagenomic data demonstrated that the YEM001 community was composed of multiple bacteria, including well-known Cr(VI)-reducing bacteria and non-Cr(VI)-reducing bacteria. Delftia, Comamonas, Alicycliphilus, Acidovorax, Bacillus, and Clostridioides account for 83% of total community abundance. The stability of the composition of the YEM001 community and its Cr(VI)-reducing activity allows for its application in bioremediation of environmental Cr(VI) pollution.},
}
@article {pmid33408878,
year = {2020},
author = {Plyusnin, I and Kant, R and Jääskeläinen, AJ and Sironen, T and Holm, L and Vapalahti, O and Smura, T},
title = {Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types.},
journal = {Virus evolution},
volume = {6},
number = {2},
pages = {veaa091},
doi = {10.1093/ve/veaa091},
pmid = {33408878},
issn = {2057-1577},
abstract = {The study of the microbiome data holds great potential for elucidating the biological and metabolic functioning of living organisms and their role in the environment. Metagenomic analyses have shown that humans, along with for example, domestic animals, wildlife and arthropods, are colonized by an immense community of viruses. The current Coronavirus pandemic (COVID-19) heightens the need to rapidly detect previously unknown viruses in an unbiased way. The increasing availability of metagenomic data in this era of next-generation sequencing (NGS), along with increasingly affordable sequencing technologies, highlight the need for reliable and comprehensive methods to manage such data. In this article, we present a novel bioinformatics pipeline called LAZYPIPE for identifying both previously known and novel viruses in host associated or environmental samples and give examples of virus discovery based on it. LAZYPIPE is a Unix-based pipeline for automated assembling and taxonomic profiling of NGS libraries implemented as a collection of C++, Perl, and R scripts.},
}
@article {pmid33408709,
year = {2020},
author = {Luo, ZH and Li, Q and Lai, Y and Chen, H and Liao, B and Huang, LN},
title = {Diversity and Genomic Characterization of a Novel Parvarchaeota Family in Acid Mine Drainage Sediments.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {612257},
doi = {10.3389/fmicb.2020.612257},
pmid = {33408709},
issn = {1664-302X},
abstract = {Recent genome-resolved metagenomic analyses of microbial communities from diverse environments have led to the discovery of many novel lineages that significantly expand the phylogenetic breadth of Archaea. Here, we report the genomic characterization of a new archaeal family based on five metagenome-assembled genomes retrieved from acid mine drainage sediments. Phylogenomic analyses placed these uncultivated archaea at the root of the candidate phylum Parvarchaeota, which expand this lesser-known phylum into two family levels. Genes involved in environmental adaptation and carbohydrate and protein utilization were identified in the ultra-small genomes (estimated size 0.53-0.76 Mb), indicating a survival strategy in this harsh environment (low pH and high heavy metal content). The detection of genes with homology to sulfocyanin suggested a potential involvement in iron cycling. Nevertheless, the absence of the ability to synthesize amino acids and nucleotides implies that these archaea may acquire these biomolecules from the environment or other community members. Applying evolutionary history analysis to Parvarchaeota suggested that members of the two families could broaden their niches by acquiring the potentials of utilizing different substrates. This study expands our knowledge of the diversity, metabolic capacity, and evolutionary history of the Parvarchaeota.},
}
@article {pmid33408706,
year = {2020},
author = {Perini, N and Mercuri, F and Orlanducci, S and Thaller, MC and Migliore, L},
title = {The Integration of Metagenomics and Chemical Physical Techniques Biodecoded the Buried Traces of the Biodeteriogens of Parchment Purple Spots.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {598945},
doi = {10.3389/fmicb.2020.598945},
pmid = {33408706},
issn = {1664-302X},
abstract = {Ancient parchments record an immense part of our cultural heritage, having been used as the main written support material for centuries. Parchment easily undergoes biodeterioration, whose main signs are the so-called purple spots, which often lead to detachment of the superficial written layer. Up to recent years, several studies have been analyzing damaged parchments from different world's archives, trying to trace back the culprit of the purple spots. However, standard cultivation and early molecular techniques have been demonstrated to be unsuccessful, leading the parchment damage issue remaining unsolved for many years. Nowadays, some studies have explored the parchment biodeterioration dynamics by adopting a multidisciplinary approach combining standard microbiological methods with high-throughput molecular, chemical and physical techniques. This approach allowed an unprecedented level of knowledge on the complex dynamics of parchment biodeterioration. This mini review discusses the application of the combination of basic and high-throughput techniques to study historical parchments, highlighting the strengths and weaknesses of this approach. In particular, it focuses on how metagenomics has been paramount for the unequivocal identification of the microbial main actors of parchment biodeterioration and their dynamics, but also on how metagenomics may suffer the distortion inflict by the historical perspective on the analysis of ancient specimens. As a whole, this mini review aims to describe the scenario of information on parchment biodeterioration obtained so far by using the integration of metagenomic with recent chemical (Raman spectroscopy) and physical (Light Transmission Analysis) approaches, which might have key implications in the preservation of many ancient documents.},
}
@article {pmid33407663,
year = {2021},
author = {Zhang, HT and Wang, H and Wu, HS and Zeng, J and Yang, Y},
title = {Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis.},
journal = {Virology journal},
volume = {18},
number = {1},
pages = {11},
pmid = {33407663},
issn = {1743-422X},
support = {F201740//Jiangsu maternal and child health project/ ; },
abstract = {BACKGROUND: Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment.<br><br>METHODS: To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis.<br><br>RESULTS: Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups.<br><br>CONCLUSION: Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.},
}
@article {pmid33407614,
year = {2021},
author = {Chi, H and Cao, W and Zhang, M and Su, D and Yang, H and Li, Z and Li, C and She, X and Wang, K and Gao, X and Ma, K and Zheng, P and Li, X and Cui, B},
title = {Environmental noise stress disturbs commensal microbiota homeostasis and induces oxi-inflammmation and AD-like neuropathology through epithelial barrier disruption in the EOAD mouse model.},
journal = {Journal of neuroinflammation},
volume = {18},
number = {1},
pages = {9},
pmid = {33407614},
issn = {1742-2094},
support = {81673136//National Natural Science Foundation of China/ ; 17JCZDJC34900//Natural Science Foundation of Tianjin City/ ; },
abstract = {BACKGROUND: Both genetic factors and environmental hazards, including environmental noise stress, have been associated with gut microbiome that exacerbates Alzheimer's disease (AD) pathology. However, the role and mechanism of environmental risk factors in early-onset AD (EOAD) pathogenesis remain unclear.<br><br>METHODS: The molecular pathways underlying EOAD pathophysiology following environmental noise exposure were evaluated using C57BL/6 wild-type (WT) and APP/PS1 Tg mouse models. The composition differences in intestinal microbiota were analyzed by 16S rRNA sequencing and Tax4Fun to predict the metagenome content from sequencing results. An assessment of the flora dysbiosis-triggered dyshomeostasis of oxi-inflamm-barrier and the effects of the CNS end of the gut-brain axis was conducted to explore the underlying pathological mechanisms.<br><br>RESULTS: Both WT and APP/PS1 mice showed a statistically significant relationship between environmental noise and the taxonomic composition of the corresponding gut microbiome. Bacterial-encoded functional categories in noise-exposed WT and APP/PS1 mice included phospholipid and galactose metabolism, oxidative stress, and cell senescence. These alterations corresponded with imbalanced intestinal oxidation and anti-oxidation systems and low-grade systemic inflammation following noise exposure. Mechanistically, axis-series experiments demonstrated that following noise exposure, intestinal and hippocampal tight junction protein levels reduced, whereas serum levels of inflammatory mediator were elevated. Regarding APP/PS1 overexpression, noise-induced abnormalities in the gut-brain axis may contribute to aggravation of neuropathology in the presymptomatic stage of EOAD mice model.<br><br>CONCLUSION: Our results demonstrate that noise exposure has deleterious effects on the homeostasis of oxi-inflamm-barrier in the microbiome-gut-brain axis. Therefore, at least in a genetic context, chronic noise may aggravate the progression of EOAD.},
}
@article {pmid33407584,
year = {2021},
author = {Avedi, EK and Adediji, AO and Kilalo, DC and Olubayo, FM and Macharia, I and Ateka, EM and Machuka, EM and Mutuku, JM},
title = {Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya.},
journal = {Virology journal},
volume = {18},
number = {1},
pages = {2},
pmid = {33407584},
issn = {1743-422X},
support = {BB/P023223/1.//UK Biotechnological and Biological Sciences Research Council GCRF/ ; },
abstract = {BACKGROUND: Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya.<br><br>METHODS: Tomato leaf samples with virus-like symptoms were obtained from farmers' field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated.<br><br>RESULTS: Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7-99.7% identity among each other and 95.9-98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5-100%) within the isolates, and 97.1-100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences.<br><br>CONCLUSIONS: The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.},
}
@article {pmid33407128,
year = {2021},
author = {Xie, Y and Sun, J and Wei, L and Jiang, H and Hu, C and Yang, J and Huang, Y and Ruan, B and Zhu, B},
title = {Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {11},
pmid = {33407128},
issn = {1471-2180},
support = {81500491//Young Scientists Fund/ ; 2018ZX10715-014//Major Research Plan/ ; },
abstract = {BACKGROUND: Although gut microbiota dysbiosis has been reported in HIV infected individuals recently, the relationship between the gut microbiota and immune activation in patients with different immune responses to highly active antiretroviral therapy (HAART) is still not well understood. Gut microbiota and immune activation were studied in 36 non-HIV-infected subjects (healthy controls) and 58 HIV-infected individuals, including 28 immunological responders (IR) and 30 immunological non-responders (INR) (≥500 and < 200 CD4+ T-cell counts/μl after 2 years of HIV-1 viral suppression respectively) without comorbidities.<br><br>RESULTS: Metagenome sequencing revealed that HIV-infected immunological responders and immunological non-responders could not recover completely from the gut microbiota dysbiosis. At a 97% similarity level, the relative abundances of Fusobacterium, Ruminococcus gnavus and Megamonas were greater, whereas Faecalibacterium, Alistipes, Bifidobacterium, Eubacterium rectale and Roseburia were more depleted in the IR and INR groups than those in the healthy controls. Ruminococcaceae and Alistipes were positively correlated with nadir and current CD4+ T-cell counts, but negatively correlated with CD8 + CD57+ T-cell counts. Inflammation markers and translocation biomarkers (LPS) levels were positively correlated with the abundances of genera Ruminococcus and Fusobacterium but were negatively correlated with the genus Faecalibacterium. The relative abundances of Escherichia-Shigella and Blautia were significantly higher in the IR than those in the INR group. Escherichia-Shigella were negatively correlated with the CD4/CD8 ratio but positively correlated with the amount of CD8 + CD57+ T-cells. Roseburia and Blautia were negatively associated with nadir CD4+ T-cell and positively associated with CD8 + CD57+ T-cell counts.<br><br>CONCLUSIONS: Gut microbiota dysbiosis may be one of the factors contributing to different immune responses and treatment outcomes to HAART.},
}
@article {pmid33407122,
year = {2021},
author = {Li, J and Si, H and Du, H and Guo, H and Dai, H and Xu, S and Wan, J},
title = {Comparison of gut microbiota structure and Actinobacteria abundances in healthy young adults and elderly subjects: a pilot study.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {13},
pmid = {33407122},
issn = {1471-2180},
abstract = {BACKGROUND: The aim was to determine the potential association of the gut microbiota composition, especially the abundance of Actinobacteria, as well as the differentiation of functional and resistance genes with age (young adults vs elderly subjects) in China.<br><br>RESULTS: The patterns of relative abundance of all bacteria isolated from fecal samples differed between young adults and elderly subjects, but the alpha diversity (Chao1 P = 0.370, Shannon P = 0.560 and Simpson P = 0.270) and beta diversity (ANOSIM R = 0.031, P = 0.226) were not significantly different. There were 3 Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways (carbon metabolism, inositol phosphate metabolism, and sesquiterpenoid and triterpenoid biosynthesis) and 7 antibiotic resistant genes (ARGs) (macrolide lincosamide-streptogramin B (MLSB), tetracycline, aminoglycoside, sulfonamide, fosmidomycin, lincomycin, and vancomycin) that showed significant differences between the 2 groups (all P < 0.05). The abundance of Actinomycetes was enriched (about 2.4-fold) in young adults. Bifidobacteria dominated in both young adults and elderly subjects, with overall higher abundances in young adults (P > 0.05). Only the Bifidobacterium_dentium species showed significant differences between the 2 groups (P = 0.013), with a higher abundance in elderly subjects but absent in young adults.<br><br>CONCLUSIONS: The present study revealed that there were 3 KEGG metabolic pathways and 7 ARGs as well as enhanced Bifidobacterium_dentium species abundance in elderly compared to young subjects.},
}
@article {pmid33407112,
year = {2021},
author = {Jing, G and Zhang, Y and Cui, W and Liu, L and Xu, J and Su, X},
title = {Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {9},
pmid = {33407112},
issn = {1471-2164},
support = {31771463//National Natural Science Foundation of China (CN)/ ; ZR201807060158//Natural Science Foundation of Shandong Province/ ; 2018M630807//China Postdoctoral Science Foundation/ ; 32070086//National Natural Science Foundation of China/ ; 32000389//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results.<br><br>RESULTS: Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS.<br><br>CONCLUSIONS: This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.},
}
@article {pmid33406597,
year = {2021},
author = {Noone, JC and Helmersen, K and Leegaard, TM and Skråmm, I and Aamot, HV},
title = {Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/microorganisms9010097},
pmid = {33406597},
issn = {2076-2607},
support = {267923//Akershus Universitetssykehus/ ; 278903 and 298904//South-Eastern Norway Regional Health Authority/ ; },
abstract = {Conventional culture-based diagnostics of orthopaedic-implant-associated infections (OIAIs) are arduous. Hence, the aim of this study was to evaluate a culture-independent, rapid nanopore-based diagnostic protocol with regard to (a) pathogen identification, (b) time to pathogen identification, and (c) identification of antimicrobial resistance (AMR). This prospective proof-of-concept study included soft tissue biopsies from 32 patients with OIAIs undergoing first revision surgery at Akershus University Hospital, Norway. The biopsies were divided into two segments. Nanopore shotgun metagenomic sequencing and pathogen and antimicrobial resistance gene identification using the EPI2ME analysis platform (Oxford Nanopore Technologies) were performed on one segment. Conventional culture-based diagnostics were performed on the other. Microbial identification matched in 23/32 OIAI patients (72%). Sequencing detected additional microbes in 9/32 patients. Pathogens detected by culturing were identified by sequencing within a median of 1 h of sequencing start [range 1-18 h]. Phenotypic AMR was explained by the detection of resistance genes in 11/23 patients (48%). Diagnostics of OIAIs using shotgun metagenomics sequencing are possible within 24 h from biopsy using nanopore technology. Sequencing outperformed culturing with respect to speed and pathogen detection where pathogens were at sufficient concentration, whereas culture-based methods had an advantage at lower pathogen concentrations. Sequencing-based AMR detection may not yet be a suitable replacement for culture-based antibiotic susceptibility testing.},
}
@article {pmid33406160,
year = {2021},
author = {Taylor, JC and Gao, X and Xu, J and Holder, M and Petrosino, J and Kumar, R and Liu, W and Höök, M and Mackenzie, C and Hillhouse, A and Brashear, W and Nunez, MP and Xu, Y},
title = {A type VII secretion system of Streptococcus gallolyticus subsp. gallolyticus contributes to gut colonization and the development of colon tumors.},
journal = {PLoS pathogens},
volume = {17},
number = {1},
pages = {e1009182},
doi = {10.1371/journal.ppat.1009182},
pmid = {33406160},
issn = {1553-7374},
abstract = {Streptococcus gallolyticus subspecies gallolyticus (Sgg) has a strong clinical association with colorectal cancer (CRC) and actively promotes the development of colon tumors. However, the molecular determinants involved in Sgg pathogenicity in the gut are unknown. Bacterial type VII secretion systems (T7SS) mediate pathogen interactions with their host and are important for virulence in pathogenic mycobacteria and Staphylococcus aureus. Through genome analysis, we identified a locus in Sgg strain TX20005 that encodes a putative type VII secretion system (designated as SggT7SST05). We showed that core genes within the SggT7SST05 locus are expressed in vitro and in the colon of mice. Western blot analysis showed that SggEsxA, a protein predicted to be a T7SS secretion substrate, is detected in the bacterial culture supernatant, indicating that this SggT7SST05 is functional. Deletion of SggT7SST05 (TX20005Δesx) resulted in impaired bacterial adherence to HT29 cells and abolished the ability of Sgg to stimulate HT29 cell proliferation. Analysis of bacterial culture supernatants suggest that SggT7SST05-secreted factors are responsible for the pro-proliferative activity of Sgg, whereas Sgg adherence to host cells requires both SggT7SST05-secreted and bacterial surface-associated factors. In a murine gut colonization model, TX20005Δesx showed significantly reduced colonization compared to the parent strain. Furthermore, in a mouse model of CRC, mice exposed to TX20005 had a significantly higher tumor burden compared to saline-treated mice, whereas those exposed to TX20005Δesx did not. Examination of the Sgg load in the colon in the CRC model suggests that SggT7SST05-mediated activities are directly involved in the promotion of colon tumors. Taken together, these results reveal SggT7SST05 as a previously unrecognized pathogenicity determinant for Sgg colonization of the colon and promotion of colon tumors.},
}
@article {pmid33406089,
year = {2021},
author = {Patumcharoenpol, P and Nakphaichit, M and Panagiotou, G and Senavonge, A and Suratannon, N and Vongsangnak, W},
title = {MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome.},
journal = {PLoS computational biology},
volume = {17},
number = {1},
pages = {e1008487},
doi = {10.1371/journal.pcbi.1008487},
pmid = {33406089},
issn = {1553-7358},
abstract = {Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.},
}
@article {pmid33404934,
year = {2021},
author = {Ali, P and Chen, F and Hassan, F and Sosa, A and Khan, S and Badshah, M and Shah, AA},
title = {Bacterial community characterization of Batura Glacier in the Karakoram Range of Pakistan.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {33404934},
issn = {1618-1905},
abstract = {High-altitude cold habitats of the Karakoram are rarely explored for their bacterial community characterization and metabolite productions. In the present study, bacterial communities in ice, water, and sediments of Batura Glacier were investigated using culture-dependent and culture-independent methods. Twenty-seven cold-adapted bacterial strains (mostly psychrotrophic) were isolated using R2A, Tryptic Soy Agar (TSA), and Luria-Bertani (LB) media, at 4 °C and 15 °C. Most of the isolates exhibited growth at a wide range of temperature (4-35 °C), pH (5-12), and salinity (1-6%). Among the bacterial isolates, 52% were identified as Gram-positive and the remaining 48% represented as Gram-negative. The results of phylogenetic analysis indicated that all the culturable bacteria belonged to 3 major phylogenetic groups, i.e., Actinobacteria (48%), Bacteroidetes (26%), and Proteobacteria (22%), while Flavobacterium (26%), Arthrobacter (22%), and Pseudomonas (19%) were represented as the dominant genera. Similarly, Illumina amplicon sequencing of 16S rRNA genes after PCR amplification of DNA from the whole community revealed dominance of the same phylogenetic groups, Proteobacteria, Actinobacteria, and Bacteroidetes, while Arthrobacter, Mycoplana, Ochrobactrum, Kaistobacter, Janthinobacterium, and Flavobacterium were found as the dominant genera. Among the culturable isolates, 70% demonstrated activity for cellulases, 48% lipases, 41% proteases, 41% DNases, and only 7% for amylases. Most of the glacial isolates demonstrated antimicrobial activity against other microorganisms including the multiple-drug-resistant strains of Candida albicans, Klebsiella pneumoniae, Acinetobacter sp., and Bacillus sp. 67% of Gram-negative while 46% of Gram-positive glacial bacteria were resistant to trimethoprim/sulfamethoxazole. Resistance against methicillin and vancomycin among the Gram-positive isolates was 23% and 15%, respectively, while 11% of the Gram-negative isolates exhibited resistance against both colistin sulfate and nalidixic acid.},
}
@article {pmid33404537,
year = {2020},
author = {Guo, X and Zhang, X and Qin, Y and Liu, YX and Zhang, J and Zhang, N and Wu, K and Qu, B and He, Z and Wang, X and Zhang, X and Hacquard, S and Fu, X and Bai, Y},
title = {Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome.},
journal = {Plant communications},
volume = {1},
number = {1},
pages = {100003},
doi = {10.1016/j.xplc.2019.100003},
pmid = {33404537},
issn = {2590-3462},
abstract = {Plant-associated microbes are critical for plant growth and survival under natural environmental conditions. To date, most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relative abundance of microbial taxa. However, this technique does not assess the total microbial load and the abundance of individual microbes relative to the amount of host plant tissues. Here, we report the development of a host-associated quantitative abundance profiling (HA-QAP) method that can accurately examine total microbial load and colonization of individual root microbiome members relative to host plants by the copy-number ratio of microbial marker gene to plant genome. We validate the HA-QAP method using mock experiments, perturbation experiments, and metagenomic sequencing. The HA-QAP method eliminates the generation of spurious outputs in the classical method based on microbial relative abundance, and reveals the load of root microbiome to host plants. Using the HA-QAP method, we found that the copy-number ratios of microbial marker genes to plant genome range from 1.07 to 6.61 for bacterial 16S rRNA genes and from 0.40 to 2.26 for fungal internal transcribed spacers in the root microbiome samples from healthy rice and wheat. Furthermore, using HA-QAP we found that an increase in total microbial load represents a key feature of changes in root microbiome of rice plants exposed to drought stress and of wheat plants with root rot disease, which significantly influences patterns of differential taxa and species interaction networks. Given its accuracy and technical feasibility, HA-QAP would facilitate our understanding of genuine interactions between root microbiome and plants.},
}
@article {pmid33402535,
year = {2021},
author = {Wilhelm, RC and Pepe-Ranney, C and Weisenhorn, P and Lipton, M and Buckley, DH},
title = {Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil.},
journal = {mBio},
volume = {12},
number = {1},
pages = {},
pmid = {33402535},
issn = {2150-7511},
abstract = {Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and 13C labeling (i.e., partial labeling or labeling at later stages). Major 13C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.IMPORTANCE Our study reveals the ecogenomic traits of microorganisms participating in the cellulose economy of soil. We identified three major categories of participants in this economy: (i) independent primary degraders, (ii) interdependent primary degraders, and (iii) secondary consumers (mutualists, opportunists, and parasites). Trade-offs between independent primary degraders, whose adaptations favor antagonism and competitive exclusion, and interdependent and secondary degraders, whose adaptations favor complex interspecies interactions, are expected to affect the fate of microbially processed carbon in soil. Our findings provide useful insights into the ecological relationships that govern one of the planet's most abundant resources of organic carbon. Furthermore, we demonstrate a novel gradient-resolved approach for stable isotope probing, which provides a cultivation-independent, genome-centric perspective into soil microbial processes.},
}
@article {pmid33401450,
year = {2021},
author = {Jalili, F and Trigui, H and Guerra Maldonado, JF and Dorner, S and Zamyadi, A and Shapiro, BJ and Terrat, Y and Fortin, N and Sauvé, S and Prévost, M},
title = {Can Cyanobacterial Diversity in the Source Predict the Diversity in Sludge and the Risk of Toxin Release in a Drinking Water Treatment Plant?.},
journal = {Toxins},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/toxins13010025},
pmid = {33401450},
issn = {2072-6651},
support = {Genome Canada/UM RQ000607//Genome Canada and Génome Québec/ ; },
abstract = {Conventional processes (coagulation, flocculation, sedimentation, and filtration) are widely used in drinking water treatment plants and are considered a good treatment strategy to eliminate cyanobacterial cells and cell-bound cyanotoxins. The diversity of cyanobacteria was investigated using taxonomic cell counts and shotgun metagenomics over two seasons in a drinking water treatment plant before, during, and after the bloom. Changes in the community structure over time at the phylum, genus, and species levels were monitored in samples retrieved from raw water (RW), sludge in the holding tank (ST), and sludge supernatant (SST). Aphanothece clathrata brevis, Microcystis aeruginosa, Dolichospermum spiroides, and Chroococcus minimus were predominant species detected in RW by taxonomic cell counts. Shotgun metagenomics revealed that Proteobacteria was the predominant phylum in RW before and after the cyanobacterial bloom. Taxonomic cell counts and shotgun metagenomic showed that the Dolichospermum bloom occurred inside the plant. Cyanobacteria and Bacteroidetes were the major bacterial phyla during the bloom. Shotgun metagenomics also showed that Synechococcus, Microcystis, and Dolichospermum were the predominant detected cyanobacterial genera in the samples. Conventional treatment removed more than 92% of cyanobacterial cells but led to cell accumulation in the sludge up to 31 times more than in the RW influx. Coagulation/sedimentation selectively removed more than 96% of Microcystis and Dolichospermum. Cyanobacterial community in the sludge varied from raw water to sludge during sludge storage (1-13 days). This variation was due to the selective removal of coagulation/sedimentation as well as the accumulation of captured cells over the period of storage time. However, the prediction of the cyanobacterial community composition in the SST remained a challenge. Among nutrient parameters, orthophosphate availability was related to community profile in RW samples, whereas communities in ST were influenced by total nitrogen, Kjeldahl nitrogen (N- Kjeldahl), total and particulate phosphorous, and total organic carbon (TOC). No trend was observed on the impact of nutrients on SST communities. This study profiled new health-related, environmental, and technical challenges for the production of drinking water due to the complex fate of cyanobacteria in cyanobacteria-laden sludge and supernatant.},
}
@article {pmid33401448,
year = {2021},
author = {Pyzik, A and Ciuchcinski, K and Dziurzynski, M and Dziewit, L},
title = {The Bad and the Good-Microorganisms in Cultural Heritage Environments-An Update on Biodeterioration and Biotreatment Approaches.},
journal = {Materials (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/ma14010177},
pmid = {33401448},
issn = {1996-1944},
support = {POIR.04.04.00-00-14E6/18-00//TEAM-NET programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund/ ; },
abstract = {Cultural heritage objects constitute a very diverse environment, inhabited by various bacteria and fungi. The impact of these microorganisms on the degradation of artworks is undeniable, but at the same time, some of them may be applied for the efficient biotreatment of cultural heritage assets. Interventions with microorganisms have been proven to be useful in restoration of artworks, when classical chemical and mechanical methods fail or produce poor or short-term effects. The path to understanding the impact of microbes on historical objects relies mostly on multidisciplinary approaches, combining novel meta-omic technologies with classical cultivation experiments, and physico-chemical characterization of artworks. In particular, the development of metabolomic- and metatranscriptomic-based analyses associated with metagenomic studies may significantly increase our understanding of the microbial processes occurring on different materials and under various environmental conditions. Moreover, the progress in environmental microbiology and biotechnology may enable more effective application of microorganisms in the biotreatment of historical objects, creating an alternative to highly invasive chemical and mechanical methods.},
}
@article {pmid33293529,
year = {2020},
author = {Wang, C and Li, H and Guo, Y and Huang, J and Sun, Y and Min, J and Wang, J and Fang, X and Zhao, Z and Wang, S and Zhang, Y and Liu, Q and Jiang, Q and Wang, X and Guo, Y and Yang, C and Wang, Y and Tian, F and Zhuang, G and Fan, Y and Gao, Q and Li, Y and Ju, Z and Li, J and Li, R and Hou, M and Yang, G and Liu, G and Liu, W and Guo, J and Pan, S and Fan, G and Zhang, W and Zhang, R and Yu, J and Zhang, X and Yin, Q and Ji, C and Jin, Y and Yue, G and Liu, M and Xu, J and Liu, S and Jordana, J and Noce, A and Amills, M and Wu, DD and Li, S and Zhou, X and Zhong, J},
title = {Donkey genomes provide new insights into domestication and selection for coat color.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {6014},
pmid = {33293529},
issn = {2041-1723},
mesh = {Animals ; *Breeding ; Chromosome Mapping ; Color ; *Domestication ; Equidae/*genetics ; Male ; Metagenomics ; Pigmentation/*genetics ; *Selection, Genetic ; Whole Genome Sequencing ; Y Chromosome/genetics ; },
abstract = {Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition.},
}
@article {pmid33067398,
year = {2020},
author = {Shibl, AA and Isaac, A and Ochsenkühn, MA and Cárdenas, A and Fei, C and Behringer, G and Arnoux, M and Drou, N and Santos, MP and Gunsalus, KC and Voolstra, CR and Amin, SA},
title = {Diatom modulation of select bacteria through use of two unique secondary metabolites.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {44},
pages = {27445-27455},
pmid = {33067398},
issn = {1091-6490},
mesh = {Animals ; Bacteria/genetics/*growth &amp; development ; Cinnamates/metabolism ; Depsides/metabolism ; Diatoms/genetics/*metabolism ; Dicarboxylic Acids/metabolism ; Gene Expression Profiling ; Metabolomics ; Metagenome ; Metagenomics ; Microbiota/*physiology ; Oceans and Seas ; Phytoplankton/genetics/*metabolism ; Secondary Metabolism/physiology ; *Water Microbiology ; },
abstract = {Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world's oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.},
}
@article {pmid33049161,
year = {2021},
author = {Khan, S and Hauptman, R and Kelly, L},
title = {Engineering the Microbiome to Prevent Adverse Events: Challenges and Opportunities.},
journal = {Annual review of pharmacology and toxicology},
volume = {61},
number = {},
pages = {159-179},
doi = {10.1146/annurev-pharmtox-031620-031509},
pmid = {33049161},
issn = {1545-4304},
abstract = {In the past decade of microbiome research, we have learned about numerous adverse interactions between the microbiome and medical interventions such as drugs, radiation, and surgery. What if we could alter our microbiomes to prevent these events? In this review, we discuss potential routes to mitigate microbiome adverse events, including applications from the emerging field of microbiome engineering. We highlight cases where the microbiome acts directly on a treatment, such as via differential drug metabolism, and cases where a treatment directly harms the microbiome, such as in radiation therapy. Understanding and preventing microbiome adverse events is a difficult challenge that will require a data-driven approach involving causal statistics, multiomics techniques, and a personalized means of mitigating adverse events. We propose research considerations to encourage productive work in preventing microbiome adverse events, and we highlight the many challenges and opportunities that await.},
}
@article {pmid31562947,
year = {2020},
author = {Hynönen, U and Zoetendal, EG and Virtala, AK and Shetty, S and Hasan, S and Jakava-Viljanen, M and de Vos, WM and Palva, A},
title = {Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut.},
journal = {Anaerobe},
volume = {62},
number = {},
pages = {102104},
doi = {10.1016/j.anaerobe.2019.102104},
pmid = {31562947},
issn = {1095-8274},
mesh = {Animals ; Cluster Analysis ; Databases, Genetic ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Mammals ; *Metagenome ; *Metagenomics/methods ; Molecular Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In our previous studies on irritable bowel syndrome (IBS) -associated microbiota by molecular methods, we demonstrated that a particular 16S rRNA gene amplicon was more abundant in the feces of healthy subjects or mixed type IBS (IBS-M) -sufferers than in the feces of individuals with diarrhea-type IBS (IBS-D). In the current study, we demonstrated that this, so called Ct85-amplicon, consists of a cluster of very heterogeneous 16S rRNA gene sequences, and defined six 16S rRNA gene types, a to f, within this cluster, each representing a novel species-, genus- or family level taxon. We then designed specific PCR primers for these sequence types, mapped the distribution of the Ct85-cluster sequences and that of the newly defined sequence types in several animal species and compared the sequence types present in the feces of healthy individuals and IBS sufferers using two IBS study cohorts, Finnish and Dutch. Various Ct85-cluster sequence types were detected in the fecal samples of several companion and production animal species with remarkably differing prevalences and abundances. The Ct85 sequence type composition of swine closely resembled that of humans. One of the five types (d) shared between humans and swine was not present in any other animals tested, while one sequence type (b) was found only in human samples. In both IBS study cohorts, one type (e) was more prevalent in healthy individuals than in the IBS-M group. By revealing various sequence types in the widespread Ct85-cluster and their distribution, the results improve our understanding of these uncultured bacteria, which is essential for future efforts to cultivate representatives of the Ct85-cluster and reveal their roles in IBS.},
}
@article {pmid31386148,
year = {2020},
author = {Maruvada, P and Lampe, JW and Wishart, DS and Barupal, D and Chester, DN and Dodd, D and Djoumbou-Feunang, Y and Dorrestein, PC and Dragsted, LO and Draper, J and Duffy, LC and Dwyer, JT and Emenaker, NJ and Fiehn, O and Gerszten, RE and B Hu, F and Karp, RW and Klurfeld, DM and Laughlin, MR and Little, AR and Lynch, CJ and Moore, SC and Nicastro, HL and O'Brien, DM and Ordovás, JM and Osganian, SK and Playdon, M and Prentice, R and Raftery, D and Reisdorph, N and Roche, HM and Ross, SA and Sang, S and Scalbert, A and Srinivas, PR and Zeisel, SH},
title = {Perspective: Dietary Biomarkers of Intake and Exposure-Exploration with Omics Approaches.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {11},
number = {2},
pages = {200-215},
pmid = {31386148},
issn = {2156-5376},
support = {K08 DK110335/DK/NIDDK NIH HHS/United States ; MR/J010308/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Biomarkers/*analysis/blood/urine ; *Diet ; Food ; Genomics ; Humans ; Metabolomics/*methods ; Metagenomics ; Nutritional Physiological Phenomena/genetics ; Nutritional Sciences/methods ; Nutritional Status ; Reproducibility of Results ; },
abstract = {While conventional nutrition research has yielded biomarkers such as doubly labeled water for energy metabolism and 24-h urinary nitrogen for protein intake, a critical need exists for additional, equally robust biomarkers that allow for objective assessment of specific food intake and dietary exposure. Recent advances in high-throughput MS combined with improved metabolomics techniques and bioinformatic tools provide new opportunities for dietary biomarker development. In September 2018, the NIH organized a 2-d workshop to engage nutrition and omics researchers and explore the potential of multiomics approaches in nutritional biomarker research. The current Perspective summarizes key gaps and challenges identified, as well as the recommendations from the workshop that could serve as a guide for scientists interested in dietary biomarkers research. Topics addressed included study designs for biomarker development, analytical and bioinformatic considerations, and integration of dietary biomarkers with other omics techniques. Several clear needs were identified, including larger controlled feeding studies, testing a variety of foods and dietary patterns across diverse populations, improved reporting standards to support study replication, more chemical standards covering a broader range of food constituents and human metabolites, standardized approaches for biomarker validation, comprehensive and accessible food composition databases, a common ontology for dietary biomarker literature, and methodologic work on statistical procedures for intake biomarker discovery. Multidisciplinary research teams with appropriate expertise are critical to moving forward the field of dietary biomarkers and producing robust, reproducible biomarkers that can be used in public health and clinical research.},
}
@article {pmid31094423,
year = {2020},
author = {Chaguza, C and Heinsbroek, E and Gladstone, RA and Tafatatha, T and Alaerts, M and Peno, C and Cornick, JE and Musicha, P and Bar-Zeev, N and Kamng'ona, A and Kadioglu, A and McGee, L and Hanage, WP and Breiman, RF and Heyderman, RS and French, N and Everett, DB and Bentley, SD},
title = {Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {70},
number = {7},
pages = {1294-1303},
pmid = {31094423},
issn = {1537-6591},
support = {MR/P011284/1/MRC_/Medical Research Council/United Kingdom ; MR/R002592/1/MRC_/Medical Research Council/United Kingdom ; R01 AI106786/AI/NIAID NIH HHS/United States ; 084679/Z/08/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Carrier State/epidemiology ; Child ; Humans ; Infant ; Malawi/epidemiology ; *Metagenomics ; Nasopharynx ; *Pneumococcal Infections/epidemiology/prevention &amp; control ; Pneumococcal Vaccines ; Serogroup ; Streptococcus pneumoniae/genetics ; Vaccines, Conjugate ; },
abstract = {BACKGROUND: Pneumococcal conjugate vaccines (PCVs) have reduced pneumococcal diseases globally. Pneumococcal genomic surveys elucidate PCV effects on population structure but are rarely conducted in low-income settings despite the high disease burden.<br><br>METHODS: We undertook whole-genome sequencing (WGS) of 660 pneumococcal isolates collected through surveys from healthy carriers 2 years from 13-valent PCV (PCV13) introduction and 1 year after rollout in northern Malawi. We investigated changes in population structure, within-lineage serotype dynamics, serotype diversity, and frequency of antibiotic resistance (ABR) and accessory genes.<br><br>RESULTS: In children <5 years of age, frequency and diversity of vaccine serotypes (VTs) decreased significantly post-PCV, but no significant changes occurred in persons ≥5 years of age. Clearance of VT serotypes was consistent across different genetic backgrounds (lineages). There was an increase of nonvaccine serotypes (NVTs)-namely 7C, 15B/C, and 23A-in children <5 years of age, but 28F increased in both age groups. While carriage rates have been recently shown to remain stable post-PCV due to replacement serotypes, there was no change in diversity of NVTs. Additionally, frequency of intermediate-penicillin-resistant lineages decreased post-PCV. Although frequency of ABR genes remained stable, other accessory genes, especially those associated with mobile genetic element and bacteriocins, showed changes in frequency post-PCV.<br><br>CONCLUSIONS: We demonstrate evidence of significant population restructuring post-PCV driven by decreasing frequency of vaccine serotypes and increasing frequency of few NVTs mainly in children under 5. Continued surveillance with WGS remains crucial to fully understand dynamics of the residual VTs and replacement NVT serotypes post-PCV.},
}
@article {pmid33401162,
year = {2021},
author = {He, X and Yin, H and Fang, C and Xiong, J and Han, L and Yang, Z and Huang, G},
title = {Metagenomic and q-PCR analysis reveals the effect of powder bamboo biochar on nitrous oxide and ammonia emissions during aerobic composting.},
journal = {Bioresource technology},
volume = {323},
number = {},
pages = {124567},
doi = {10.1016/j.biortech.2020.124567},
pmid = {33401162},
issn = {1873-2976},
abstract = {To investigate the emission mechanism of ammonia (NH3) and nitrous oxide (N2O) during aerobic composting and the influence of powder bamboo biochar (PBB) on this process, this paper conducted a systematic study on the nitrogen-transforming functional microbial community, including functional genes, microbial structure and metabolism pathways. PBB reduced N2O and NH3 emissions by 1.25%-8.72% and 10.4%-11.8%, respectively. The quantitative PCR results indicated that the reduced N2O emission by PBB were mainly related to denitrifying genes (nirS, nirK, nosZ, and narG). The metagenome results demonstrated that Nitrosococcus was the main genus that could oxidize ammonia to nitrite decreased by PBB. The PBB significantly affected the nitrogen metabolism pathway, reduced the activity of glutamate dehydrogenase to inhibit the formation of NH4+ to reduce NH3 emission. The higher N2O emission in the control group was also related to the higher relative contents of hydroxylamine reductase and nitrite reductase.},
}
@article {pmid33401045,
year = {2020},
author = {Zhu, X and Chen, Y and Liu, X and Li, D},
title = {Effects of higher temperature on antibiotic resistance genes for in-situ biogas upgrading reactors with H2 addition.},
journal = {The Science of the total environment},
volume = {764},
number = {},
pages = {144639},
doi = {10.1016/j.scitotenv.2020.144639},
pmid = {33401045},
issn = {1879-1026},
abstract = {In-situ biogas upgrading by H2 injection is a promising method for bio-natural gas production, yet the effect of H2 addition on antibiotic resistance genes during the in-situ biogas upgrading process remains unknown. We analyzed mesophilic and thermophilic in-situ biogas upgrading digesters with intermittent or continuous mixing models using metagenomic and metatranscriptomic methods to evaluate the effects of H2 addition on antibiotic resistance profiles. We found that H2 addition had less impact in the mesophilic reactor. In the thermophilic reactor, the influenced antibiotic resistance ontology (AROs) was mostly bound to the integral membrane transporters of the ATP-binding cassette and major facilitator superfamily. The annotated gene numbers of four drug classes, including macrolide, glycopeptide, lincosamide, and fluoroquinolone, increased distinctly after H2 addition. Acetate concentration is a vital indicator for distinguishing the abundance of different antibiotic efflux pumps. Most of the AROs influenced by Ruminiclostridium replaced the original dominant species Clostridium, and the versatile genus Methanosarcina was the sole methanogen correlated with the altered AROs of efflux pumps conferring antibiotic resistance. The introduced H2 was synthesized to CH4via the hydrogenotrophic pathway of Methanosarcina flavescens, and part of the consumed H2 was used for cell growth.},
}
@article {pmid33400377,
year = {2021},
author = {Singh, A and Schnürer, A and Westerholm, M},
title = {Enrichment and description of novel bacteria performing syntrophic propionate oxidation at high ammonia level.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15388},
pmid = {33400377},
issn = {1462-2920},
abstract = {Inefficient syntrophic propionate degradation causes severe operating disturbances and reduces biogas productivity in many high-ammonia anaerobic digesters, but propionate-degrading microorganisms in these systems remain unknown. Here, we identified candidate ammonia-tolerant syntrophic propionate-oxidising bacteria using propionate enrichment at high ammonia levels (0.7-0.8 g NH3 /L) in continuously-fed reactors. We reconstructed 30 high-quality metagenome-assembled genomes (MAGs) from the propionate-fed reactors, which revealed two novel species from the families Peptococcaceae and Desulfobulbaceae as syntrophic propionate-oxidising candidates. Both MAGs possess genomic potential for the propionate oxidation and electron transfer required for syntrophic energy conservation and, similar to ammonia-tolerant acetate degrading syntrophs, both MAGs contain genes predicted to link to ammonia and pH tolerance. Based on relative abundance, a Peptococcaceae sp. appeared to be the main propionate degrader and has been given the provisional name &quot;Candidatus Syntrophopropionicum ammoniitolerans&quot;. This bacterium was also found in high-ammonia biogas digesters, using quantitative PCR. Acetate was degraded by syntrophic acetate-oxidising bacteria and the hydrogenotrophic methanogenic community consisted of Methanoculleus bourgensis and a yet to be characterised Methanoculleus sp. This work provides knowledge of cooperating syntrophic species in high-ammonia systems and reveals that ammonia-tolerant syntrophic propionate-degrading populations share common features, but diverge genomically and taxonomically from known species. This article is protected by copyright. All rights reserved.},
}
@article {pmid33400089,
year = {2021},
author = {Shi, J and Shen, S and Wu, H and Zhang, Y and Deng, F},
title = {Metagenomic Profiling of Viruses Associated with Rhipicephalus microplus Ticks in Yunnan Province, China.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
pmid = {33400089},
issn = {1995-820X},
abstract = {Ticks are well known as vectors of many viruses which usually do great harm to human and animal health. Yunnan Province, widely covered by flourishing vegetation and mainly relying on farming husbandry, is abundant with Rhipicephalus microplus ticks. Therefore, it is of great significance to characterize the viral profile present in R. microplus parasitizing on cattle in Yunnan Province. In this study, a total of 7387 R. microplus ticks were collected from cattle and buffalo in the northwest and southeast areas of Yunnan Province from 2015 to 2017. We investigated the virome of R. microplus using next-generation sequencing (NGS) and the prevalence of important identified viruses among tick groups by RT-PCR. It revealed the presence of diverse virus concerning chu-, rhabdo-, phlebo-, flavi- and parvo- viruses in Yunnan. These viruses consist of single-stranded, circular and segmented sense RNAs, showing a greatly diversity in genomic organization. Furthermore, continuous epidemiological survey among ticks reveals broad prevalence of three viruses (Yunnan mivirus 1, Wuhan tick vrius 1 and YN tick-associated phlebovirus 1) and two possible prevalent viruses including a flavivirus-like segmented virus (Jingmen tick virus) and a bovine hokovirus 2 in Yunnan. Serological investigation among cattle indicates that these identified viruses may be infectious to cattle and can elicit corresponding antibody. Our findings on R. microplus-associated viral community will contribute to the prevention of viral disease and tracking the viral evolution. Further analysis is needed to better elucidate the pathogenicity and natural circulation of these viruses.},
}
@article {pmid33398958,
year = {2020},
author = {Tan, Y and Hu, H and Li, C and Luo, X and Tan, Y and Dai, L},
title = {[Research progress and applications of strain analysis based on metagenomic data].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {36},
number = {12},
pages = {2610-2621},
doi = {10.13345/j.cjb.200380},
pmid = {33398958},
issn = {1872-2075},
abstract = {Strain is the fundamental unit in microbial taxonomy. The functional diversity among strains has great influence on host phenotypes. With the development of microbiome research, knowing the composition and functional capacities of complex microbial communities at the strain level has become increasingly valuable in scientific research and clinical applications. This review introduces the principles of bioinformatics algorithms for strain analysis based on metagenomic data, the applications in microbiome research and directions of future development.},
}
@article {pmid33398957,
year = {2020},
author = {Liu, D and Zhang, C and Wang, Y and Xu, S},
title = {[Challenges and considerations on quality control and evaluation of pathogen metagenomic next-generation sequencing].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {36},
number = {12},
pages = {2598-2609},
doi = {10.13345/j.cjb.200377},
pmid = {33398957},
issn = {1872-2075},
abstract = {Metagenomic next-generation sequencing (mNGS) could be used for pathogen detection from nearly all types of clinical samples. Especially, the unique diagnostic capability of pathogen mNGS detecting unknown causative agent of infectious diseases makes this method become an importation complement and irreplaceable component for conventional routine laboratory test. However, the complexity of the testing process, the rapid product update, and the insufficiency in quality control and evaluation methods that all make clinical transformation, industry development, and regulation of this technology full of challenge and uncertainty. This review briefly introduces the technical advantages and challenges, and describes the general workflow and quality control steps in details. Finally, it focuses on current considerations regarding quality evaluation methods and standards for pathogen mNGS.},
}
@article {pmid33398955,
year = {2020},
author = {Zhang, Y and Cao, J and Zhao, N and Wang, J},
title = {[Virome: the next hotspot in microbiome research].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {36},
number = {12},
pages = {2566-2581},
doi = {10.13345/j.cjb.200372},
pmid = {33398955},
issn = {1872-2075},
abstract = {Virome is the collective term for the viral collection or viral metagenomes that are distributed in various environments. Viruses can be found in bodies of water, glaciers, plants, animals, and even some viruses, which are classified as eukaryotes, prokaryotes and subviruses. Viruses play very important role in maintaining environmental homeostasis and ecosystem balance, and are especially closely related to human health. In recent years, with the advancement of sequencing technology and data analysis, we are able to gain more insights into the virome and explore its potential role in the ecological niche by metagenomic sequencing. A large amount of viral data have been obtained from glaciers, oceans, and various plants and animals, and numerous unknown viruses have been discovered. Virome has been studied mainly through metagenomic data mining, as well as virus-like particles separation and enrichment. To date, several different methods for viral isolation and enrichment exist, and numerous bioinformatic analyses of the virome have been performed. However, there is a lack of specific and complete reviews on the enrichment and data analysis methods for the virome. Thus, our review will summarize viral isolation and enrichment methods and data analysis, and present some of the landmark research conducted by the enrichment method, to provide a reference for researchers of interest and further advance the field of virome research.},
}
@article {pmid33398952,
year = {2020},
author = {Chen, T and Zhang, T and Yang, Y and Zhao, B and Wu, C},
title = {[Quantification of microbial DNA in laboratory environment during DNA extraction].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {36},
number = {12},
pages = {2541-2547},
doi = {10.13345/j.cjb.200526},
pmid = {33398952},
issn = {1872-2075},
abstract = {Metagenomic sequencing provides a powerful tool for microbial research. However, traditional experimental DNA extraction process will inevitably mix with environmental microorganisms which float in the air. It is still unclear whether the mixed environmental microbial DNA will heavily affect the metagenomic results of samples with extremely low microbial content. In this study, we first collected environmental bacteria in the laboratory and quantified the mixed environmental microbial DNA content during DNA extraction based on a qPCR-based quantification assay. We then extracted DNA from pure water in order to determine the mixed microbial taxons during extraction under open environment. At last, we extracted total DNA from a skin sample in a Biosafety cabinet or under open laboratory environment, to assess the impact of the mixed environmental microorganisms on the metagenomic results. Our results showed that DNA extraction under open laboratory environment in Beijing region resulted in 28.9 pg contaminant, which may accout for 30% of total DNA amount from skin samples. Metagenomic analysis revealed that the main incorporated environmental taxons were Cutibacterium acnes and Escherichia coli. Tens of environmental bacteria were foisted in the skin DNA samples, which largely decreased the relative abundance of dominant species and thus deteriorated the result accuracy. Therefore, analyzing microbial composition of samples with extremely low DNA content should better performed under aseptic environment.},
}
@article {pmid33398949,
year = {2020},
author = {Duan, Y and Zhu, B},
title = {[Preface for microbiome sequencing and analysis].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {36},
number = {12},
pages = {2511-2515},
doi = {10.13345/j.cjb.200800},
pmid = {33398949},
issn = {1872-2075},
abstract = {Microbes are the most important commensal organisms in humans, animals and plants, and are the major habitants in soil, sediment, water, air and other habitats. The analysis of microbiome in these habitats has become a basic research technique. As a fast developing technology in recent years, microbiome sequencing and analysis have been widely used in human health, environmental pollution control, food industry, agriculture and animal husbandry and other fields. In order to sort out and summarize the current status, development and application prospects of microbiome sequencing and analysis technologies, this special issue has prepared a collection of 16 papers in this field, that comprise sample preservation and processing, single microbe genome sequencing and analysis, and microbiome feature analysis in special habitats, microbiome related databases and algorithms, and microbiome sequencing and analysis expert consensus. It also introduced in detail the development trend of the microbiome sequencing and analysis, in order to promote the rapid development of the microbiome sequencing and analysis industry and scientific research in China, and provide necessary reference for the healthy development of related industries.},
}
@article {pmid33398809,
year = {2021},
author = {Inoue, K},
title = {Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins.},
journal = {Advances in experimental medicine and biology},
volume = {1293},
number = {},
pages = {89-126},
pmid = {33398809},
issn = {0065-2598},
abstract = {Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H+, Na+, Cl-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.},
}
@article {pmid33398153,
year = {2021},
author = {Nissen, JN and Johansen, J and Allesøe, RL and Sønderby, CK and Armenteros, JJA and Grønbech, CH and Jensen, LJ and Nielsen, HB and Petersen, TN and Winther, O and Rasmussen, S},
title = {Improved metagenome binning and assembly using deep variational autoencoders.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {33398153},
issn = {1546-1696},
support = {NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
abstract = {Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that uses deep variational autoencoders to encode sequence coabundance and k-mer distribution information before clustering. We show that a variational autoencoder is able to integrate these two distinct data types without any previous knowledge of the datasets. VAMB outperforms existing state-of-the-art binners, reconstructing 29-98% and 45% more near-complete (NC) genomes on simulated and real data, respectively. Furthermore, VAMB is able to separate closely related strains up to 99.5% average nucleotide identity (ANI), and reconstructed 255 and 91 NC Bacteroides vulgatus and Bacteroides dorei sample-specific genomes as two distinct clusters from a dataset of 1,000 human gut microbiome samples. We use 2,606 NC bins from this dataset to show that species of the human gut microbiome have different geographical distribution patterns. VAMB can be run on standard hardware and is freely available at https://github.com/RasmussenLab/vamb .},
}
@article {pmid33398096,
year = {2021},
author = {Bay, SK and Dong, X and Bradley, JA and Leung, PM and Grinter, R and Jirapanjawat, T and Arndt, SK and Cook, PLM and LaRowe, DE and Nauer, PA and Chiri, E and Greening, C},
title = {Trace gas oxidizers are widespread and active members of soil microbial communities.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {33398096},
issn = {2058-5276},
support = {NSFC//National Natural Science Foundation of China (National Science Foundation of China)/ ; P2EZP3_178421//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; DP180101762//Department of Education and Training | Australian Research Council (ARC)/ ; DP180101762//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; NE/T010967/1//RCUK | Natural Environment Research Council (NERC)/ ; Foundation Fellowship//Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation)/ ; },
abstract = {Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how soil microbial communities meet energy and carbon needs. Analysis of 40 metagenomes and 757 derived genomes indicated that over 70% of soil bacterial taxa encode enzymes to consume inorganic energy sources. Bacteria from 19 phyla encoded enzymes to use the trace gases hydrogen and carbon monoxide as supplemental electron donors for aerobic respiration. In addition, we identified a fourth phylum (Gemmatimonadota) potentially capable of aerobic methanotrophy. Consistent with the metagenomic profiling, communities within soil profiles from diverse habitats rapidly oxidized hydrogen, carbon monoxide and to a lesser extent methane below atmospheric concentrations. Thermodynamic modelling indicated that the power generated by oxidation of these three gases is sufficient to meet the maintenance needs of the bacterial cells capable of consuming them. Diverse bacteria also encode enzymes to use trace gases as electron donors to support carbon fixation. Altogether, these findings indicate that trace gas oxidation confers a major selective advantage in soil ecosystems, where availability of preferred organic substrates limits microbial growth. The observation that inorganic energy sources may sustain most soil bacteria also has broad implications for understanding atmospheric chemistry and microbial biodiversity in a changing world.},
}
@article {pmid33398049,
year = {2021},
author = {Niederdorfer, R and Hausherr, D and Palomo, A and Wei, J and Magyar, P and Smets, BF and Joss, A and Bürgmann, H},
title = {Temperature modulates stress response in mainstream anammox reactors.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {23},
pmid = {33398049},
issn = {2399-3642},
abstract = {Autotrophic nitrogen removal by anaerobic ammonium oxidizing (anammox) bacteria is an energy-efficient nitrogen removal process in wastewater treatment. However, full-scale deployment under mainstream conditions remains challenging for practitioners due to the high stress susceptibility of anammox bacteria towards fluctuations in dissolved oxygen (DO) and temperature. Here, we investigated the response of microbial biofilms with verified anammox activity to DO shocks under 20 °C and 14 °C. While pulse disturbances of 0.3 mg L-1 DO prompted only moderate declines in the NH4+ removal rates, 1.0 mg L-1 DO led to complete but reversible inhibition of the NH4+ removal activity in all reactors. Genome-centric metagenomics and metatranscriptomics were used to investigate the stress response on various biological levels. We show that temperature regime and strength of DO perturbations induced divergent responses from the process level down to the transcriptional profile of individual taxa. Community-wide gene expression differed significantly depending on the temperature regime in all reactors, and we found a noticeable impact of DO disturbances on genes involved in transcription, translation, replication and posttranslational modification at 20 °C but not 14 °C. Genome-centric analysis revealed that different anammox species and other key biofilm taxa differed in their transcriptional responses to distinct temperature regimes and DO disturbances.},
}
@article {pmid33397904,
year = {2021},
author = {Yahara, K and Suzuki, M and Hirabayashi, A and Suda, W and Hattori, M and Suzuki, Y and Okazaki, Y},
title = {Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {27},
pmid = {33397904},
issn = {2041-1723},
abstract = {Bacteriophages (phages), or bacterial viruses, are very diverse and highly abundant worldwide, including as a part of the human microbiomes. Although a few metagenomic studies have focused on oral phages, they relied on short-read sequencing. Here, we conduct a long-read metagenomic study of human saliva using PromethION. Our analyses, which integrate both PromethION and HiSeq data of >30 Gb per sample with low human DNA contamination, identify hundreds of viral contigs; 0-43.8% and 12.5-56.3% of the confidently predicted phages and prophages, respectively, do not cluster with those reported previously. Our analyses demonstrate enhanced scaffolding, and the ability to place a prophage in its host genomic context and enable its taxonomic classification. Our analyses also identify a Streptococcus phage/prophage group and nine jumbo phages/prophages. 86% of the phage/prophage group and 67% of the jumbo phages/prophages contain remote homologs of antimicrobial resistance genes. Pan-genome analysis of the phages/prophages reveals remarkable diversity, identifying 0.3% and 86.4% of the genes as core and singletons, respectively. Furthermore, our study suggests that oral phages present in human saliva are under selective pressure to escape CRISPR immunity. Our study demonstrates the power of long-read metagenomics utilizing PromethION in uncovering bacteriophages and their interaction with host bacteria.},
}
@article {pmid33397696,
year = {2021},
author = {Arntzen, MØ and Pedersen, B and Klau, LJ and Stokke, R and Oftebro, M and Antonsen, SG and Fredriksen, L and Sletta, H and Aarstad, OA and Aachmann, FL and Horn, SJ and Eijsink, VGH},
title = {Insights into alginate degradation through the characterization of a thermophilic exolytic alginate lyase.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02399-20},
pmid = {33397696},
issn = {1098-5336},
abstract = {Enzymatic depolymerization of seaweed polysaccharides is gaining interest for the production of functional oligosaccharides and fermentable sugars. Herein, we describe a thermostable alginate lyase that belongs to Polysaccharide Lyase family 17 (PL17) and was derived from an Arctic Mid-Ocean Ridge (AMOR) metagenomics dataset. This enzyme, AMOR_PL17A, is a thermostable exolytic oligoalginate lyase (EC 4.2.2.26), which can degrade alginate, poly β-d-mannuronate and poly α-l-guluronate within a broad range of pH, temperature and salinity conditions. Site-directed mutagenesis showed that tyrosine Y251, previously suggested to act as catalytic acid, indeed is essential for catalysis; whereas mutation of tyrosine Y446, previously proposed to act as catalytic base, did not affect enzyme activity. The observed reaction products are protonated and deprotonated forms of the 4,5-unsaturated uronic acid monomer, Δ, two hydrates of DEH (4-deoxy-l-erythro-5-hexulosuronate), which are formed after ring opening and, finally, two epimers of a 5-membered hemiketal called 4-deoxy-d-manno-hexulofuranosidonate (DHF) formed through intramolecular cyclisation of hydrated DEH. The detection and NMR assignment of these hemiketals refine our current understanding of alginate degradation.Importance The potential markets for seaweed-derived products and seaweed processing technologies are growing, yet commercial enzyme-cocktails for complete conversion of seaweed to fermentable sugars are not available. Such an enzyme-cocktail would require the catalytic properties of a variety of different enzymes, where fucoidanases, laminarinases and cellulases together with endo- and exo-acting alginate lyases would be the key enzymes. Here we present an exo-acting alginate lyase that efficiently produces monomeric sugars from alginate. Since it is only the second characterized exo-acting alginate lyase capable of degrading alginate at industrially relevant higher temperatures of 60 °C, this enzyme may be of great biotechnological and industrial interest. In addition, in-depth NMR-based structural elucidation reveal previously undescribed rearrangement products of the unsaturated monomeric sugars generated from exo-acting lyases. The insight provided by the NMR assignment of these products facilitates future assessment of product formation by alginate lyases.},
}
@article {pmid33397500,
year = {2021},
author = {LaPelusa, M and Donoviel, D and Branzini, SE and Carlson, PE and Culler, S and Cheema, AK and Kaddurah-Daouk, R and Kelly, D and de Cremoux, I and Knight, R and Krajmalnik-Brown, R and Mayo, SL and Mazmanian, SK and Mayer, EA and Petrosino, JF and Garrison, K},
title = {Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {2},
pmid = {33397500},
issn = {2049-2618},
support = {NNX16AO69A//Translational Research Institute for Space Health (TRISH)/ ; },
abstract = {The inaugural &quot;Microbiome for Mars&quot; virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duration human space travel. The conference focused on surveying current microbiome research, future endeavors, and how this growing field could broadly impact human health and space exploration. This report summarizes each speaker's presentation in the order presented at the workshop.},
}
@article {pmid33397406,
year = {2021},
author = {Zhang, R and Walker, AR and Datta, S},
title = {Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge.},
journal = {Biology direct},
volume = {16},
number = {1},
pages = {1},
pmid = {33397406},
issn = {1745-6150},
support = {1UL1TR000064/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Composition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the whole genome shotgun (WGS) metagenomics data from samples across 16 cities around the world and samples from another 8 cities were provided as the main and mystery datasets respectively as the part of the CAMDA 2019 MetaSUB &quot;Forensic Challenge&quot;. The feature selecting, normalization, three methods of machine learning, PCoA (Principal Coordinates Analysis) and ANCOM (Analysis of composition of microbiomes) were conducted for both the main and mystery datasets.<br><br>RESULTS: Features selecting, combined with the machines learning methods, revealed that the combination of the common features was effective for predicting the origin of the samples. The average error rates of 11.93 and 30.37% of three machine learning methods were obtained for main and mystery datasets respectively. Using the samples from main dataset to predict the labels of samples from mystery dataset, nearly 89.98% of the test samples could be correctly labeled as &quot;mystery&quot; samples. PCoA showed that nearly 60% of the total variability of the data could be explained by the first two PCoA axes. Although many cities overlapped, the separation of some cities was found in PCoA. The results of ANCOM, combined with importance score from the Random Forest, indicated that the common &quot;family&quot;, &quot;order&quot; of the main-dataset and the common &quot;order&quot; of the mystery dataset provided the most efficient information for prediction respectively.<br><br>CONCLUSIONS: The results of the classification suggested that the composition of the microbiomes was distinctive across the cities, which could be used to identify the sample origins. This was also supported by the results from ANCOM and importance score from the RF. In addition, the accuracy of the prediction could be improved by more samples and better sequencing depth.},
}
@article {pmid33397232,
year = {2021},
author = {Hajiagha, MN and Taghizadeh, S and Asgharzadeh, M and Dao, S and Ganbarov, K and Köse, Ş and Kafil, HS},
title = {Gut microbiota And Human Body Interactions; Its Impact on Health: a review.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/1389201022666210104115836},
pmid = {33397232},
issn = {1873-4316},
abstract = {Gut microbiota (GM) as an organ of the human body has a particular and autonomous function that related to it. This review aimed to investigate human intestinal and gut microbiota interaction and its impact on health. As a creation referable database about this dynamic and complex organ, several comprehensive projects are implemented by using culture-dependent (culturomics), culture independent methods (e.g metagenomics, mathematics model), and Gnotobiological together. This study was done by searching PubMed, Scopus and Google scholar database in the gut, health microbiota and interaction keywords. The first acquired microbiota during pregnancy or childbirth is colonized in the gut by using specific and non-specific mechanisms. That`s structure and shape reach relative stability with selection pressure along with host development until adulthood and keep its resilience against external or internal variables depending on the host genetics and negative feedback. Due to several research individuals have 2 functional group microbiota including the core (common between vast majorities human) and flexible (transient population) microbiome. The most important role of the GM in the human body can be summarized in three basic landscapes: metabolic, immune system, and gut-brain axis interaction. So that loss of microbial population balance will lead to disorder and disease.},
}
@article {pmid33397125,
year = {2021},
author = {BenIsrael, M and Habtewold, JZ and Khosla, K and Wanner, P and Aravena, R and Parker, BL and Haack, EA and Tsao, DT and Dunfield, KE},
title = {Identification of degrader bacteria and fungi enriched in rhizosphere soil from a toluene phytoremediation site using DNA stable isotope probing.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/15226514.2020.1860901},
pmid = {33397125},
issn = {1549-7879},
abstract = {Improved knowledge of the ecology of contaminant-degrading organisms is paramount for effective assessment and remediation of aromatic hydrocarbon-impacted sites. DNA stable isotope probing was used herein to identify autochthonous degraders in rhizosphere soil from a hybrid poplar phytoremediation system incubated under semi-field-simulated conditions. High-throughput sequencing of bacterial 16S rRNA and fungal internal transcribed spacer (ITS) rRNA genes in metagenomic samples separated according to nucleic acid buoyant density was used to identify putative toluene degraders. Degrader bacteria were found mainly within the Actinobacteria and Proteobacteria phyla and classified predominantly as Cupriavidus, Rhodococcus, Luteimonas, Burkholderiaceae, Azoarcus, Cellulomonadaceae, and Pseudomonas organisms. Purpureocillium lilacinum and Mortierella alpina fungi were also found to assimilate toluene, while several strains of the fungal poplar endophyte Mortierella elongatus were indirectly implicated as potential degraders. Finally, PICRUSt2 predictive taxonomic functional modeling of 16S rRNA genes was performed to validate successful isolation of stable isotope-labeled DNA in density-resolved samples. Four unique sequences, classified within the Bdellovibrionaceae, Intrasporangiaceae, or Chitinophagaceae families, or within the Sphingobacteriales order were absent from PICRUSt2-generated models and represent potentially novel putative toluene-degrading species. This study illustrates the power of combining stable isotope amendment with advanced metagenomic and bioinformatic techniques to link biodegradation activity with unisolated microorganisms. Novelty statement: This study used emerging molecular biological techniques to identify known and new organisms implicated in aromatic hydrocarbon biodegradation from a field-scale phytoremediation system, including organisms with phyto-specific relevance and having potential for downstream applications (amendment or monitoring) in future and existing systems. Additional novelty in this study comes from the use of taxonomic functional modeling approaches for validation of stable isotope probing techniques. This study provides a basis for expanding existing reference databases of known aromatic hydrocarbon degraders from field-applicable sources and offers technological improvements for future site assessment and management purposes.},
}
@article {pmid33397001,
year = {2021},
author = {Huang, MX and Ye, B and Jiang, Y and Tang, LF and Chen, ZM},
title = {[Pulmonary actinomycosis in children: a case report and literature review].},
journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics},
volume = {59},
number = {1},
pages = {33-36},
doi = {10.3760/cma.j.cn112140-20200430-00453},
pmid = {33397001},
issn = {0578-1310},
support = {81801552//National Natural Science Foundation of China/ ; },
abstract = {Objective: To summarize the clinical characteristics, imaging features, diagnosis, treatment and prognosis of pulmonary actinomycosis in children. Methods: The clinical data of a child with pulmonary actinomycosis who was hospitalized in Children's Hospital, Zhejiang University School of Medicine in December 2019 was retrospectively analyzed. The related literature published from January 1975 to January 2020 was retrieved from Wanfang, CNKI and PubMed databases with &quot;pulmonary&quot; or &quot;thoracic&quot; and &quot;actinomycosis&quot; and &quot;pediatric&quot; or &quot;children&quot; or &quot;child&quot; as the keywords. And the characteristics of pediatric pulmonary actinomycosis were summarized based on the literature review. Results: The patient was a boy aged 12 years and 6 months. He was admitted due to cough and chest pain for more than 20 days, with fever on the first three days. The chest CT scan in local hospital found inflammatory lesions in the right middle lobe, which was also suspected to be cavitation. The flexible bronchoscopy showed congestion and edema of bronchial mucosa in the right middle lobe, and bronchoalveolar lavage fluid smear was positive for acid-fast bacilli DNA, although both purfied protein derivatives tuberculin test and T-spot were negative. During the hospitalization, the child had persistent cough and chest pain, but no fever. Pathogen metagene sequencing of the bronchoalveolar lavage fluid detected Actinomyces (sequence number: 222) and Grevini Actinomycetes (sequence number: 185). The boy received intravenous cefoperazone sulbactam sodium for 2 weeks followed by oral amoxicillin clavulanate potassium for 6 weeks. Until April 2020, his clinical symptoms completely relieved, and the pulmonary lesions were significantly absorbed on the latest chest CT scan. Eight articles and 62 children with pulmonary actinomycosis were reported, but no related reports were retrieved from CNKI and Wanfang databases. The youngest case was 27 months old. The clinical presentations of this disease were nonspecific. The main symptoms included chest wall masses (8 cases), cough (23 cases), pain (chest, back, shoulders and armpits) (24 cases), fever (25 cases), weight loss (26 cases), etc. Conclusions: The clinical manifestations and imaging features of pediatric pulmonary actinomycosis are nonspecific, therefore it could easily be misdiagnosed. For children with pneumonia of unknown etiology and failing to respond to routine antibiotics, the pathogen metagene sequencing of the bronchoalveolar lavage fluid will be helpful for diagnosis. With appropriate course of antibiotic treatment, the prognosis is good in most cases.},
}
@article {pmid33396998,
year = {2021},
author = {Huang, H and Chen, Y and Ma, LY and Yan, MM and Deng, Y and Zhang, WD and Yuan, Y and Xiong, P and Fang, F and Liu, TL},
title = {[Analysis of the clinical features and the risk factors of severe adenovirus pneumonia in children].},
journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics},
volume = {59},
number = {1},
pages = {14-19},
doi = {10.3760/cma.j.cn112140-20200704-00687},
pmid = {33396998},
issn = {0578-1310},
support = {2018CFB746//Natural Science Foundation of Hubei Province/ ; },
abstract = {Objective: To analyze the clinical characteristics, risk factors for critical illness and death of severe adenovirus pneumonia in children, so as to provide clinical evidences for early diagnosis and reliable treatment. Methods: A total of 75 pediatric cases with severe adenovirus pneumonia admitted to Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology from January to October 2019 were studied. The clinical features, laboratory and imaging data, therapeutic approaches, efficacy of the treatments and prognosis were investigated retrospectively. Patients were divided into severe group and critical group. Chi square test and Mann-Whitney U rank sum test were used to analyze the data of the two groups. The risk factors for critical illness and death were analyzed by univariate and multivariate Logistic regression. Results: Among the 75 children, there were 52 males and 23 females, aged from 3 months to 8 years, including 30 of severe cases and 45 of critical case. The positive rate of adenovirus antigen in nasopharyngeal swab was 21% (15/72), and the positive rate of serum adenovirus IgM antibody was only 13% (10/75). However, the positive rate of adenovirus nucleic acid in nasopharyngeal swab was 75% (21/28). What is more, the positive rates of metagenomics next generation sequencing (mNGS) in plasma and bronchoalveolar lavage fluid were 92% (33/36) and 96% (54/56), respectively, of which 95% (63/66) were confirmed as adenovirus type 7. Relatively high dose of ribavirin and integrated therapeutic approaches (respiratory support, glucocorticoids, immunoglobulin and organ supportive therapies) were used. The recovery rate was 77% (58/75), the improvement rate was 8% (6/75) and the mortality rate was 15% (11/75). The proportion of children with the duration of fever longer than 3 days after ribavirin treatment in the critical group was significantly higher than that in the severe group(51% (18/35) vs. 8% (2/26), χ2=12.949, P<0.05). The risk factors for critical illness were younger than 4 years, longer duration of fever before and after admission to PICU, oxygenation index<300 mmHg (1 mm Hg=0.133 kPa), ferritin>1 000 μg/L, lactate dehydrogenase (LDH)>1 500 U/L, 5 lung lobes involvement, pleural effusion and (or) air leakage (all P<0.05). Among them, 5 lung lobes involvement was the independent risk factor for critical illness (adjusted OR=49.641, 95%CI 4.186-588.618, P=0.002). Risk factors for death included longer duration of fever after being admitted to PICU, oxygenation index<100 mmHg, ferritin>2 000 μg/L, interleukin (IL)-6>100 ng/L, LDH>1 500 U/L, pleural effusion and (or) air leakage (all P<0.05). Among them, IL-6>100 ng/L was the independent risk factor for the mortalities of critically ill children (adjusted OR=16.094, 95%CI 2.059-25.787, P=0.008). Conclusions: The mortality rate of severe pediatric adenovirus pneumonia caused by adenovirus type 7 is high. High positive rates of adenovirus nucleic acid in nasopharyngeal swabs and mNGS in plasma or bronchoalveolar lavage fluid contribute to early diagnosis, and mNGS can also be used for serotyping. Younger children under 4 years of age, persistent fever, extensive pulmonary lesions and significantly increased inflammatory cytokines such as IL-6 are warning indicators for critical illness and poor prognosis. Relatively high dose of ribavirin combined with integrated therapeutic approaches are beneficial for prognosis.},
}
@article {pmid33396683,
year = {2020},
author = {Kuramae, EE and Dimitrov, MR and da Silva, GHR and Lucheta, AR and Mendes, LW and Luz, RL and Vet, LEM and Fernandes, TV},
title = {On-Site Blackwater Treatment Fosters Microbial Groups and Functions to Efficiently and Robustly Recover Carbon and Nutrients.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/microorganisms9010075},
pmid = {33396683},
issn = {2076-2607},
support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 2013/50351-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 206884/2014-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 99999.008090/2015-07;0622/2014//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.},
}
@article {pmid33396411,
year = {2020},
author = {Nzila, A and Musa, MM},
title = {Current Status of and Future Perspectives in Bacterial Degradation of Benzo[a]pyrene.},
journal = {International journal of environmental research and public health},
volume = {18},
number = {1},
pages = {},
doi = {10.3390/ijerph18010262},
pmid = {33396411},
issn = {1660-4601},
support = {IN171022//King Fahd University of Petroleum and Minerals/ ; },
abstract = {Benzo[a]pyrene (BaP) is one the main pollutants belonging to the high-molecular-weight PAHs (HMW-PAHs) class and its degradation by microorganisms remains an important strategy for its removal from the environment. Extensive studies have been carried out on the isolation and characterisation of microorganisms that can actively degrade low-molecular-weight PAHs (LMW-PAHs), and to a certain extent, the HMW-PAH pyrene. However, so far, limited work has been carried out on BaP biodegradation. BaP consists of five fused aromatic rings, which confers this compound a high chemical stability, rendering it less amenable to biodegradation. The current review summarizes the emerging reports on BaP biodegradation. More specifically, work carried out on BaP bacterial degradation and current knowledge gaps that limit our understanding of BaP degradation are highlighted. Moreover, new avenues of research on BaP degradation are proposed, specifically in the context of the development of &quot;omics&quot; approaches.},
}
@article {pmid33395796,
year = {2019},
author = {Ma, KL and Li, XK and Bao, LL},
title = {Influence of organic loading rate on purified terephthalic acid wastewater treatment in a temperature staged anaerobic treatment (TSAT) system: Performance and metagenomic characteristics.},
journal = {Chemosphere},
volume = {220},
number = {},
pages = {1091-1099},
doi = {10.1016/j.chemosphere.2019.01.028},
pmid = {33395796},
issn = {1879-1298},
abstract = {In this study, a temperature staged anaerobic treatment (TSAT) system featured by thermophilic reactor (R1)-mesophilic reactor (R2) co-digestion was introduced to treat PTA wastewater. The process was successively conducted at three organic loading rates (OLRs): 3.34, 4.45, 6.68 kg COD/(m³·d), respectively (OLRs were R1 basis). The results indicated that TSAT system was highly efficient in PTA wastewater treatment at OLR lower than 4.45 kg COD/(m³·d). Miseq sequencing analysis demonstrated that R1 and R2 were predominated by hydrogenotrophic Methanolinea and acetotrophic Methanosaeta, separately. In addition, TA06, Caldisericia and Acetothermia associated groups were highly abundant in R1, whereas Chlorobiaceae and Syntrophobacteraceae were largely observed in R2. Tax4Fun analysis suggested that the important functional capabilities were significantly different between R1 and R2 (P < 0.05). The pathways related to aromatic compounds degradation mainly occurred in mesophilic stage, while the biosynthesis and metabolism pathways were more favored in thermophilic stage.},
}
@article {pmid33395690,
year = {2021},
author = {Muturi, SM and Muthui, LW and Njogu, PM and Onguso, JM and Wachira, FN and Opiyo, SO and Pelle, R},
title = {Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0244755},
doi = {10.1371/journal.pone.0244755},
pmid = {33395690},
issn = {1932-6203},
abstract = {The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate's versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities' metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities' abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its' productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.},
}
@article {pmid33395552,
year = {2020},
author = {Zhu, Z and Cao, M and Wang, W and Zhang, L and Ma, T and Liu, G and Zhang, Y and Shang, Z and Chen, X and Shi, Y and Zhang, J},
title = {Exploring the Prevalence and Distribution Patterns of Antibiotic Resistance Genes in Bovine Gut Microbiota Using a Metagenomic Approach.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1089/mdr.2020.0271},
pmid = {33395552},
issn = {1931-8448},
abstract = {Antibiotic resistance genes (ARGs) have become recognized contaminants and pose a high public health risk. The animal gut microbiota is a reservoir of ARGs, but the knowledge of the origin and dissemination of ARGs remains unclear. In this study, we provide a comprehensive profile of ARGs and mobile genetic elements in the gut microbiota from 30 bovines to study the impact of modern antibiotics on resistance. A total of 42 ARG types were detected by annotating the metagenomic sequencing data from Comprehensive Antibiotic Resistance Database (CARD). We found that the diversity and abundance of ARGs in individual yaks were significantly lower than those in dairy and beef cattle (p < 0.0001). The results of heat map and single nucleotide polymorphism clustering suggest that ARGs from dairy and beef cattle are more similar, whereas those from yaks cluster separately. The long-term use of antibiotics may contribute to this difference, suggesting that antibiotic consumption is the main cause of ARG prevalence. Furthermore, abundant insertions were also found in this study, signifying a strong potential for horizontal transfer of ARGs among microbes, especially pathogens.},
}
@article {pmid33395419,
year = {2021},
author = {Macher, JN and Prazeres, M and Taudien, S and Jompa, J and Sadekov, A and Renema, W},
title = {Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0244616},
doi = {10.1371/journal.pone.0244616},
pmid = {33395419},
issn = {1932-6203},
abstract = {Foraminifera are a group of mostly marine protists with high taxonomic diversity. Species identification is often complex, as both morphological and molecular approaches can be challenging due to a lack of unique characters and reference sequences. An integrative approach combining state of the art morphological and molecular tools is therefore promising. In this study, we analysed large benthic Foraminifera of the genus Amphisorus from Western Australia and Indonesia. Based on previous findings on high morphological variability observed in the Soritidae and the discontinuous distribution of Amphisorus along the coast of western Australia, we expected to find multiple morphologically and genetically unique Amphisorus types. In order to gain detailed insights into the diversity of Amphisorus, we applied micro CT scanning and shotgun metagenomic sequencing. We identified four distinct morphotypes of Amphisorus, two each in Australia and Indonesia, and showed that each morphotype is a distinct genotype. Furthermore, metagenomics revealed the presence of three dinoflagellate symbiont clades. The most common symbiont was Fugacium Fr5, and we could show that its genotypes were mostly specific to Amphisorus morphotypes. Finally, we assembled the microbial taxa associated with the two Western Australian morphotypes, and analysed their microbial community composition. Even though each Amphisorus morphotype harboured distinct bacterial communities, sampling location had a stronger influence on bacterial community composition, and we infer that the prokaryotic community is primarily shaped by the microhabitat rather than host identity. The integrated approach combining analyses of host morphology and genetics, dinoflagellate symbionts, and associated microbes leads to the conclusion that we identified distinct, yet undescribed taxa of Amphisorus. We argue that the combination of morphological and molecular methods provides unprecedented insights into the diversity of foraminifera, which paves the way for a deeper understanding of their biodiversity, and facilitates future taxonomic and ecological work.},
}
@article {pmid33394429,
year = {2021},
author = {Thakur, B and Yadav, R and Mukherjee, A and Melayah, D and Marmeisse, R and Fraissinet-Tachet, L and Reddy, MS},
title = {Protection from metal toxicity by Hsp40-like protein isolated from contaminated soil using functional metagenomic approach.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {33394429},
issn = {1614-7499},
support = {4709-1//Indo-French Centre for the Promotion of Advanced Research/ ; },
abstract = {Pollution in the environment due to accumulation of potentially toxic metals results in deterioration of soil and water quality, thus impacting health of all living organisms including microbes. In the present investigation, a functional metagenomics approach was adopted to mine functional genes involved in metal tolerance from potentially toxic metal contaminated site. Eukaryotic cDNA library (1.0-4.0 kb) was screened for the genes providing tolerance to cadmium (Cd) toxicity through a functional complementation assay using Cd-sensitive Saccharomyces cerevisiae mutant ycf1Δ. Out of the 98 clones able to recover growth on Cd-supplemented selective medium, one clone designated as PLCc43 showed more tolerance to Cd along with some other clones. Sequence analysis revealed that cDNA PLCc43 encodes a 284 amino acid protein harbouring four characteristic zinc finger motif repeats (CXXCXGXG) and showing partial homology with heat shock protein (Hsp40) of Acanthamoeba castellanii. qPCR analysis revealed the induction of PLCc43 in the presence of Cd, which was further supported by accumulation of Cd in ycf1Δ/PLCc43 mutant. Cu-sensitive (cup1Δ), Zn-sensitive (zrc1Δ) and Co-sensitive (cot1Δ) yeast mutant strains were rescued from sensitivity when transformed with cDNA PLCc43 indicating its ability to confer tolerance to various potentially toxic metals. Oxidative stress tolerance potential of PLCc43 was also confirmed in the presence of H2O2. Present study results suggest that PLCc43 originating from a functional eukaryotic gene of soil community play an important role in detoxification of potentially toxic metals and may be used as biomarker in various contaminated sites.},
}
@article {pmid33394404,
year = {2021},
author = {Li, Q and Yu, S and Yang, S and Yang, W and Que, S and Li, W and Qin, Y and Yu, W and Jiang, H and Zhao, D},
title = {Eukaryotic community diversity and pathogenic eukaryotes in a full-scale drinking water treatment plant determined by 18S rRNA and metagenomic sequencing.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {33394404},
issn = {1614-7499},
support = {No. YRWEF201903//Foundation of Key Laboratory of Yangtze River Water Environment, Ministry of Education (Tongji University), China/ ; No. KJQN201900715//the Science and Technology Research Program of Chongqing Municipal Education Commission/ ; No. 19JDKJC-A019//Starting Research Foundation from Chongqing Jiaotong University/ ; No. 19JDKJC-C023//Starting Research Foundation from Chongqing Jiaotong University/ ; },
abstract = {In this study, 18S rRNA high-throughput sequencing was applied to investigate the eukaryotic community in a full-scale drinking water treatment plant. Eukaryotic species and microbial functions in raw water and filter biofilms were identified by metagenomic sequencing. The eukaryotic species richness and diversity presented declining trends throughout the treatment process. The lowest eukaryotic species richness was observed in disinfected water. Arthropoda, Ciliophora, Ochrophyta, and Rotifera were the dominant eukaryotic phyla and exhibited high variations in relative abundance among the different treatment units. Sedimentation significantly decreased the abundance of all eukaryotes except Arthropoda. Biological activated carbon (BAC) filtration and chlorine disinfection exerted strong effects on community composition. The eukaryotic communities in water were distinct from those in filter biofilms, as were the communities of different filter biofilms from each other. In contrast, communities were functionally similar among different filter biofilms, with the category metabolism being the dominant category represented, within which amino acid transport and metabolism (E) and energy production and conversion (C) dominated among subcategories. Seventy-one eukaryotic species pathogenic to humans were identified in raw water and filter biofilms. Quantitative PCR (qPCR) results showed that Acanthamoeba spp. and Vermamoeba vermiformis were present during some treatment processes, with concentrations of 12-1.2 × 105 copies/mL and 1 copy/mL, respectively. Neither of the two pathogenic amoebae was found in disinfected water. Canonical correspondence analysis (CCA) showed that pH was the most important environmental factor affecting eukaryotic community composition. Overall, the results provide insights into the eukaryotic community diversity in drinking water treatment plants and the potential eukaryotic hazards involved in drinking water production.},
}
@article {pmid33394148,
year = {2021},
author = {Lozo, J and Topisirovic, L and Kojic, M},
title = {Natural bacterial isolates as an inexhaustible source of new bacteriocins.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {33394148},
issn = {1432-0614},
support = {451-03-68/2020-14/ 200178 and 451-03-68/2020-14/ 200042//Ministry of Education, Science and Technological Development of the Republic of Serbia/ ; },
abstract = {Microorganisms isolated from various traditionally fermented food products prepared in households without commercial starter cultures are designated as natural isolates. In addition, this term is also used for microorganisms collected from various natural habitats or products (silage, soil, manure, plant and animal material, etc.) that do not contain any commercial starters or bacterial formulations. They are characterized by unique traits that are the result of the selective pressure of environmental conditions, as well as interactions with other organisms. The synthesis of antimicrobial molecules, including bacteriocins, is an evolutionary advantage and an adaptive feature that sets them apart from other microorganisms from a common environment. This review aims to underline the knowledge of bacteriocins produced by natural isolates, with a particular emphasis on the most common location of their genes and operons, plasmids, and the importance of the relationship between the plasmidome and the adaptive potential of the isolate. Applications of bacteriocins, ranging from natural food preservatives to supplements and drugs in pharmacology and medicine, will also be addressed. The latest challenges faced by researchers in isolating new natural isolates with desired characteristics will be discussed, as well as the production of new antimicrobials, nearly one century since the first discovery of colicins in 1925. KEY POINTS: • Natural bacterial isolates harbor unique properties shaped by diverse interactions. • Horizontal gene transfer enables constant engineering of new antimicrobials. • Fermented food products are important source of bacteriocin-producing natural isolates.},
}
@article {pmid33392758,
year = {2021},
author = {Liu, J and Hao, W and He, Z and Kwek, E and Zhu, H and Ma, N and Ma, KY and Chen, ZY},
title = {Blueberry and cranberry anthocyanin extracts reduce bodyweight and modulate gut microbiota in C57BL/6 J mice fed with a high-fat diet.},
journal = {European journal of nutrition},
volume = {},
number = {},
pages = {},
pmid = {33392758},
issn = {1436-6215},
support = {14105820//General Research Fund/ ; },
abstract = {PURPOSE: Blueberry and cranberry are rich in anthocyanins. The present study was to investigate the effects of anthocyanin extracts from blueberry and cranberry on body weight and gut microbiota.<br><br>METHODS: C57BL/6 J Mice were divided into six groups (n = 9 each) fed one of six diets namely low-fat diet (LFD), high-fat diet (HFD), HFD with the addition of 1% blueberry extract (BL), 2% blueberry extract (BH), 1% cranberry extract (CL), and 2% cranberry extract (CH), respectively.<br><br>RESULTS: Feeding BL and BH diets significantly decreased body weight gain by 20-23%, total adipose tissue weight by 18-20%, and total liver lipids by 16-18% compared with feeding HFD. Feeding CH diet but not CL diet reduced the body weight by 27%, accompanied by a significant reduction of total plasma cholesterol by 25% and tumor necrosis factor alpha (TNF-α) by 38%. The metagenomic analysis showed that the supplementation of blueberry and cranberry anthocyanin extracts reduced plasma lipopolysaccharide concentration, accompanied by a reduction in the relative abundance of Rikenella and Rikenellaceae. Dietary supplementation of berry anthocyanin extracts promoted the growth of Lachnoclostridium, Roseburia, and Clostridium_innocuum_group in genus level, leading to a greater production of fecal short-chain fatty acids (SCFA).<br><br>CONCLUSIONS: It was concluded that both berry anthocyanins could manage the body weight and favorably modulate the gut microbiota at least in mice.},
}
@article {pmid33392673,
year = {2021},
author = {Choudhary, JS and Naaz, N and Prabhakar, CS and Das, B and Singh, AK and Bhatt, BP},
title = {High Taxonomic and Functional Diversity of Bacterial Communities Associated with Melon Fly, Zeugodacus cucurbitae (Diptera: Tephritidae).},
journal = {Current microbiology},
volume = {},
number = {},
pages = {},
pmid = {33392673},
issn = {1432-0991},
abstract = {The next generation sequencing (NGS) approach has facilitated the investigations of gut microbiota with high throughput and resolution. The present study was focused on the taxonomic and functional characterization of bacterial community associated with different developmental stages of melon fly, Zeugodacus cucurbitae using 16S ribosomal RNA (rRNA) gene amplicons metagenomics. Z. cucurbitae is considered an invasive and most staid polyphagous pest of cucurbitaceous and other related crops. The taxonomic analysis of highly variable V3-V4 region of bacterial 16S rRNA gene sequencing indicated that the bacterial community associated with Z. cucurbitae consists of a total of 23 bacterial phyla (including unclassified and unassigned bacteria), comprising 32 classes, 69 orders, 99 families and 130 genera. Proteobacteria, Firmicutes, Actinobacteria and Tenericutes were dominant phyla of which family, Enterobacteriaceae was the most abundant in the larval and adult female stages, whereas Mycoplasmataceae was the dominant in the pupal stage. In larval stages of Z. cucurbitae, genus Providencia and Comamonas were the most abundant. However, genus Candidatus-Bacilloplasma and Klebsiella were the most dominant in pupae and adult females of Z. cucurbitae, respectively. PICRUSt analysis conducted for prediction of metabolic activities revealed that associated microbiota were involved in membrane transport, carbohydrate metabolism, amino acid metabolism, energy metabolism, replication and repair processes as well as cellular processes and signalling. The higher number of OTUs was annotated for phosphoglycerate mutase and transketolase in adult females followed by larval stages, which may support the digestive function of the microbiota in larvae and adult females. Our findings provide insights about the high variation in microbiota across developmental stages and basis for microbiota-based management strategies of fruit flies.},
}
@article {pmid33392237,
year = {2020},
author = {Yang, M and Yang, X and Chen, X and Wang, J and Liao, Z and Wang, L and Zhong, Q and Fang, X},
title = {Effect of Kefir on Soybean Isoflavone Aglycone Content in Soymilk Kefir.},
journal = {Frontiers in nutrition},
volume = {7},
number = {},
pages = {587665},
doi = {10.3389/fnut.2020.587665},
pmid = {33392237},
issn = {2296-861X},
abstract = {Kefir is a traditional fermented milk originating in the Caucasus area and parts of Eastern Europe. In this study, the kefir culture, which is modified upon the addition of lactic acid bacteria (LAB) cells, specifically for soymilk kefir fermentation with the highest capacity of isoflavone biotransformation, was successfully produced, and the metagenomics composition of soymilk or milk fermented using these kefir cultures was investigated. The metagenome analysis showed that the microbiota of kefir in M-K (milk inoculated with kefir), SM-K (equal volumes of soymilk and milk inoculated with kefir), and S-K (pure milk inoculated with kefir) were related to the addition of soymilk or not. Furthermore, the HPLC chromatogram revealed that Guixia 2 (Guangzhou, China) may be a good source of soymilk kefir fermentation due to its high isoflavone aglycone content (90.23 ± 1.26 μg/g in daidzein, 68.20 ± 0.74 μg/g in genistein). Importantly, the starter culture created by adding 1.5 g probiotics (Biostime®, Guangzhou, China) to Chinese kefir showed a significant increase in the levels of isoflavone aglycones (72.07 ± 0.53 μg/g in isoflavone aglycones). These results provided insight into understanding the suitable soybean cultivar and starter cultures, which exhibit promising results of isoflavone biotransformation and flavor promotion during soymilk kefir fermentation.},
}
@article {pmid33392236,
year = {2020},
author = {Bailén, M and Bressa, C and Martínez-López, S and González-Soltero, R and Montalvo Lominchar, MG and San Juan, C and Larrosa, M},
title = {Microbiota Features Associated With a High-Fat/Low-Fiber Diet in Healthy Adults.},
journal = {Frontiers in nutrition},
volume = {7},
number = {},
pages = {583608},
doi = {10.3389/fnut.2020.583608},
pmid = {33392236},
issn = {2296-861X},
abstract = {A high intake of dietary saturated fatty acids (SFAs) is related to an increased risk of obesity, inflammation and cancer-related diseases, and this risk is attenuated only when SFAs are replaced by unsaturated fats and unrefined carbohydrates. The gut microbiota has recently emerged as a new environmental factor in the pathophysiology of these disorders, and is also one of the factors most influenced by diet. We sought to determine whether the gut microbiota of healthy individuals whose intake of SFAs exceeds World Health Organization (WHO) recommendations exhibits features similar to those reported in people with obesity, inflammation, cancer or metabolic disease. Healthy non-obese subjects were divided into two groups based on their SFAs intake. Body composition and gut microbiota composition were analyzed, and associations between bacterial taxa, diet and body fat composition were determined globally and separately by sex. Metagenome functional pathways were predicted by PICRUSt analysis. Subjects whose SFAs intake exceeded WHO recommendations also had a dietary pattern of low fiber intake. This high saturated fat/low fiber diet was associated with a greater sequence abundance of the Anaerotruncus genus, a butyrate producer associated with obesity. Analysis of data of high SFAs intake by sex showed that females presented with a greater abundance of Campylobacter, Blautia, Flavonifractor and Erysipelatoclostridium, whereas males showed higher levels of Anaerotruncus, Eisenbergiella, a genus from the order Clostridiales (FamilyXIIIUCG_001) and two genera from the Lachnospiraceae family. PICRUSt analysis confirmed these data, showing a correlation with a decrease in the abundance of sequences encoding for transporters of some metals such as iron, which is needed to maintain a healthy metabolism. Thus, the microbiota of healthy people on a high SFAs diet contain bacterial taxa (Anaerotruncus, Lachnospiraceae Flavonifractor, Campylobacter, Erysipelotrichacea and Eisenbergiella) that could be related to the development of some diseases, especially obesity and other pro-inflammatory diseases in women. In summary, the present study identifies bacterial taxa that could be considered as early predictors for the onset of different diseases in healthy subjects. Also, sex differences in gut microbiota suggest that women and men differentially benefit from following a specific diet.},
}
@article {pmid33392172,
year = {2020},
author = {Askri, R and Erable, B and Etcheverry, L and Saadaoui, S and Neifar, M and Cherif, A and Chouchane, H},
title = {Allochthonous and Autochthonous Halothermotolerant Bioanodes From Hypersaline Sediment and Textile Wastewater: A Promising Microbial Electrochemical Process for Energy Recovery Coupled With Real Textile Wastewater Treatment.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {8},
number = {},
pages = {609446},
doi = {10.3389/fbioe.2020.609446},
pmid = {33392172},
issn = {2296-4185},
abstract = {The textile and clothing industry is the first manufacture sector in Tunisia in terms of employment and number of enterprises. It generates large volumes of textile dyeing wastewater (TDWW) containing high concentrations of saline, alkaline, and recalcitrant pollutants that could fuel tenacious and resilient electrochemically active microorganisms in bioanodes of bioelectrochemical systems. In this study, a designed hybrid bacterial halothermotolerant bioanode incorporating indigenous and exogenous bacteria from both hypersaline sediment of Chott El Djerid (HSCE) and TDWW is proposed for simultaneous treatment of real TDWW and anodic current generation under high salinity. For the proposed halothermotolerant bioanodes, electrical current production, chemical oxygen demand (COD) removal efficiency, and bacterial community dynamics were monitored. All the experiments of halothermotolerant bioanode formation have been conducted on 6 cm2 carbon felt electrodes polarized at -0.1 V/SCE and inoculated with 80% of TDWW and 20% of HSCE for 17 days at 45°C. A reproducible current production of about 12.5 ± 0.2 A/m2 and a total of 91 ± 3% of COD removal efficiency were experimentally validated. Metagenomic analysis demonstrated significant differences in bacterial diversity mainly at species level between anodic biofilms incorporating allochthonous and autochthonous bacteria and anodic biofilm containing only autochthonous bacteria as a control. Therefore, we concluded that these results provide for the first time a new noteworthy alternative for achieving treatment and recover energy, in the form of a high electric current, from real saline TDWW.},
}
@article {pmid33391225,
year = {2020},
author = {Takizawa, S and Asano, R and Fukuda, Y and Feng, M and Baba, Y and Abe, K and Tada, C and Nakai, Y},
title = {Change of Endoglucanase Activity and Rumen Microbial Community During Biodegradation of Cellulose Using Rumen Microbiota.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {603818},
doi = {10.3389/fmicb.2020.603818},
pmid = {33391225},
issn = {1664-302X},
abstract = {Treatment with rumen microorganisms improves the methane fermentation of undegradable lignocellulosic biomass; however, the role of endoglucanase in lignocellulose digestion remains unclear. This study was conducted to investigate endoglucanases contributing to cellulose degradation during treatment with rumen microorganisms, using carboxymethyl cellulose (CMC) as a substrate. The rate of CMC degradation increased for the first 24 h of treatment. Zymogram analysis revealed that endoglucanases of 52 and 53 kDa exhibited high enzyme activity for the first 12 h, whereas endoglucanases of 42, 50, and 101 kDa exhibited high enzyme activities from 12 to 24 h. This indicates that the activities of these five endoglucanases shifted and contributed to efficient CMC degradation. Metagenomic analysis revealed that the relative abundances of Selenomonas, Eudiplodinium, and Metadinium decreased after 12 h, which was positively correlated with the 52- and 53-kDa endoglucanases. Additionally, the relative abundances of Porphyromonas, Didinium, unclassified Bacteroidetes, Clostridiales family XI, Lachnospiraceae and Sphingobacteriaceae increased for the first 24 h, which was positively correlated with endoglucanases of 42, 50, and 101 kDa. This study suggests that uncharacterized and non-dominant microorganisms produce and/or contribute to activity of 40, 50, 52, 53, and 101 kDa endoglucanases, enhancing CMC degradation during treatment with rumen microorganisms.},
}
@article {pmid33391216,
year = {2020},
author = {Rosales, E and Del Olmo, G and Calero Preciado, C and Douterelo, I},
title = {Phosphate Dosing in Drinking Water Distribution Systems Promotes Changes in Biofilm Structure and Functional Genetic Diversity.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {599091},
doi = {10.3389/fmicb.2020.599091},
pmid = {33391216},
issn = {1664-302X},
abstract = {Water utilities treat drinking water by adding phosphate to prevent metal dissolution from water pipe work systems and particularly lead poisoning. Phosphate can be a limiting nutrient for microbial biofilms in DWDS, yet its effects on these microbial consortia are not well understood. This research presents results from phosphate dosing experiments using a real scale chlorinated DWDS, comparing standard phosphate concentrations of United Kingdom drinking water (1 mgP/L) with a double dose (2 mgP/L) commonly used in plumbosolvency treatment. Biofilm development during phosphate treatment experiments was monitored using a holistic approach by combining metagenomics analysis, flow cytometry and SEM characterisation. The increase of phosphate levels in drinking water, reduced biofilm cell numbers and promoted the presence of poorly distributed biofilms on inner pipe surfaces. Metagenomics analysis using genetic markers (16S rRNA and ITS2) showed that phosphate influenced biofilm community structure, particularly fungal composition. Whole metagenome sequencing showed that phosphate enrichment favoured the presence of sequencing reads associated to ATPases, ion transporters and DNA-interacting proteins, whilst reads associated to nitrogen metabolism were predominant in control samples. This research brings new knowledge regarding the influence of phosphate treatment on the composition and structure of biofilms within DWDS, and the implications that this might have for the management of these systems.},
}
@article {pmid33391191,
year = {2020},
author = {Alves, JI and Salvador, AF and Castro, AR and Zheng, Y and Nijsse, B and Atashgahi, S and Sousa, DZ and Stams, AJM and Alves, MM and Cavaleiro, AJ},
title = {Long-Chain Fatty Acids Degradation by Desulfomonile Species and Proposal of &quot;Candidatus Desulfomonile Palmitatoxidans&quot;.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {539604},
doi = {10.3389/fmicb.2020.539604},
pmid = {33391191},
issn = {1664-302X},
abstract = {Microbial communities with the ability to convert long-chain fatty acids (LCFA) coupled to sulfate reduction can be important in the removal of these compounds from wastewater. In this work, an enrichment culture, able to oxidize the long-chain fatty acid palmitate (C16:0) coupled to sulfate reduction, was obtained from anaerobic granular sludge. Microscopic analysis of this culture, designated HP culture, revealed that it was mainly composed of one morphotype with a typical collar-like cell wall invagination, a distinct morphological feature of the Desulfomonile genus. 16S rRNA gene amplicon and metagenome-assembled genome (MAG) indeed confirmed that the abundant phylotype in HP culture belong to Desulfomonile genus [ca. 92% 16S rRNA gene sequences closely related to Desulfomonile spp.; and ca. 82% whole genome shotgun (WGS)]. Based on similar cell morphology and average nucleotide identity (ANI) (77%) between the Desulfomonile sp. in HP culture and the type strain Desulfomonile tiedjei strain DCB-1T, we propose a novel species designated as &quot;Candidatus Desulfomonile palmitatoxidans.&quot; This bacterium shares 94.3 and 93.6% 16S rRNA gene identity with Desulfomonile limimaris strain DCB-MT and D. tiedjei strain DCB-1T, respectively. Based on sequence abundance of Desulfomonile-morphotype in HP culture, its predominance in the microscopic observations, and presence of several genes coding for enzymes involved in LCFA degradation, the proposed species &quot;Ca. Desulfomonile palmitatoxidans&quot; most probably plays an important role in palmitate degradation in HP culture. Analysis of the growth of HP culture and D. tiedjei strain DCB-1T with short- (butyrate), medium- (caprylate) and long-chain fatty acids (palmitate, stearate, and oleate) showed that both cultures degraded all fatty acids coupled to sulfate reduction, except oleate that was only utilized by HP culture. In the absence of sulfate, neither HP culture, nor D. tiedjei strain DCB-1T degraded palmitate when incubated with Methanobacterium formicicum as a possible methanogenic syntrophic partner. Unlike D. tiedjei strain DCB-1T, &quot;Ca. Desulfomonile palmitatoxidans&quot; lacks reductive dehalogenase genes in its genome, and HP culture was not able to grow by organohalide respiration. An emended description of the genus Desulfomonile is proposed. Our study reveals an unrecognized LCFA degradation feature of the Desulfomonile genus.},
}
@article {pmid33277504,
year = {2020},
author = {Tian, L and Wang, XW and Wu, AK and Fan, Y and Friedman, J and Dahlin, A and Waldor, MK and Weinstock, GM and Weiss, ST and Liu, YY},
title = {Deciphering functional redundancy in the human microbiome.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {6217},
pmid = {33277504},
issn = {2041-1723},
support = {UH3 OD023268/OD/NIH HHS/United States ; U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Algorithms ; Bacteria/classification/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Genetic ; },
abstract = {Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved - implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network - a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient's pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.},
}
@article {pmid33389354,
year = {2021},
author = {Rimoldi, S and Antonini, M and Gasco, L and Moroni, F and Terova, G},
title = {Intestinal microbial communities of rainbow trout (Oncorhynchus mykiss) may be improved by feeding a Hermetia illucens meal/low-fishmeal diet.},
journal = {Fish physiology and biochemistry},
volume = {},
number = {},
pages = {},
pmid = {33389354},
issn = {1573-5168},
support = {2016-01-01//This research was partially funded by AGER, Network Foundation, Project Fine Feed for Fish (4F)./ ; 818367.//This work was also co-funded by the EU Horizon 2020 AquaIMPACT (Genomic and nutritional Innovations for genetically superior farmed fish to improve efficiency in European aquaculture)/ ; },
abstract = {With demands and reliance on aquaculture still growing, there are various challenges to allow sustainable growth and the shift from fishmeal (FM) to other protein sources in aquafeed formulations is one of the most important. In this regard, interest in the use of insect meal (IM) in aquafeeds has grown rapidly. Accordingly, the aim of the present study was to assess the effects of dietary IM from Hermetia illucens (Hi) larvae included in a low-FM diet on gut microbial communities of rainbow trout (Oncorhynchus mykiss), in terms of both composition and function of microbiome. A feeding trial was conducted using 192 trout of about 100-g mean initial weight. Fish were fed in quadruplicate (4 tanks/diet) for 131 days with two diets: the control (Ctrl) contained 20% of FM as well as other protein sources, whereas the Hi diet contained 15% of Hi larvae meal to replace 50% of the FM contained in the Ctrl diet. High-throughput sequencing of 16S rRNA gene was used to identify the major feed and gut bacterial taxa, whereas Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis was performed on gut bacterial genomes to identify the major active biological pathways. The inclusion of IM led to an increase in Firmicutes, mainly represented by Bacilli class and to a drastic reduction of Proteobacteria. Beneficial genera, such as Lactobacillus and Bacillus, were enriched in the gut of fish fed with the Hi diet, whereas the number of bacteria assigned to the pathogenic Aeromonas genus was drastically reduced in the same fish group. The metagenome functional data provided evidence that dietary IM inclusion can shape the metabolic activity of trout gut microbiota. In particular, intestinal microbiome of fish fed with IM may have the capacity to improve dietary carbohydrate utilization. Therefore, H. illucens meal is a promising protein source for trout nutrition, able to modulate gut microbial community by increasing the abundance of some bacteria taxa that are likely to play a key role in fish health.},
}
@article {pmid33389103,
year = {2021},
author = {Zhou, L and Hu, C and Zhou, Q and Yang, D and Wang, L and Zhang, B},
title = {Viral communities associated with porcine diarrhoeal disease and genetic characterization of a bufavirus in Tibetan pigs in China.},
journal = {Archives of virology},
volume = {},
number = {},
pages = {},
pmid = {33389103},
issn = {1432-8798},
support = {31772766//the National Natural Science Foundation of China/ ; 2020YJ0247//the Sichuan Science and Technology Program/ ; 20yyjs0030//the Application Fundamental Research Program of Ganzi Tibetan Autonomous Prefecture/ ; 2020NQN30//the Fundamental Research Funds for the Central Universities of Southwest Minzu University/ ; },
abstract = {To investigate the viral communities in diarrhoeal faeces of Tibetan pigs, 146 diarrhoeic samples were collected from 16 pigs farms on the Tibetan plateau. Nineteen viruses belonging to eleven viral taxonomic families were identified in a pooled library. Metagenomics analysis revealed that the viruses were mainly small linear and circular DNA viruses. Furthermore, sequences of 10 NS1 genes and two complete genomes of PBuVs were obtained by PCR amplification. Sequence comparisons and phylogenetic analysis showed that the PBuVs from Tibetan pigs displayed more abundant genetic diversity than those from domestic pigs. This is the first description of the faecal viral community in Tibetan pigs associated with diarrhoea.},
}
@article {pmid33388628,
year = {2020},
author = {Zhao, X and Li, X and Li, Y and Zhang, X and Zhai, F and Ren, T and Li, Y},
title = {Metagenomic analysis reveals functional genes in soil microbial electrochemical removal of tetracycline.},
journal = {Journal of hazardous materials},
volume = {408},
number = {},
pages = {124880},
doi = {10.1016/j.jhazmat.2020.124880},
pmid = {33388628},
issn = {1873-3336},
abstract = {Microbial fuel cells (MFCs) are capable of removing tetracycline in soils, in which the degradation efficiency of tetracycline is hindered by its strong adsorption capacity. Phosphate was chosen as a competitor for tetracycline adsorption to improve its removal rate in soil MFCs. The results showed that 42-50% of tetracycline was degraded within 7 days, which was 42-67% higher than open-circuit treatments. Compared with closed-circuit treatments without phosphate addition, the removal efficiencies of tetracycline after phosphate addition increased by 19-25% on day 51, and accumulated charge outputs were enhanced by 31-52%, while the abundance of antibiotic resistance genes decreased by 19-27%. Like Geobacter, the abundance of Desulfurispora and Anaeroomyxobacter in the anode showed similar tendencies with current densities, suggesting their dominant roles in bioelectricity generation. Gemmatimonadetes bacterium SCN 70-22, Azohydromonas australica, Steroidobacter denitrificans and Gemmatirosa kalamazoonesis were found to be potential electrotrophic microbes in the cathode. The expressed flavoprotein 2,3-oxidoreductase, quinol oxidase and fumarate reductase might have promoted the transfer efficiency of electrons from cathodes to cells, which finally accelerated the biodegradation rate of tetracycline in addition to the polyphenol oxidase. This study provides an insight into functional enzyme genes in the soil microbial electrochemical remediation.},
}
@article {pmid33387530,
year = {2020},
author = {Kummen, M and Thingholm, LB and Rühlemann, MC and Holm, K and Hansen, SH and Moitinho-Silva, L and Liwinski, T and Zenouzi, R and Storm-Larsen, C and Midttun, Ø and McCann, A and Ueland, PM and Høivik, ML and Vesterhus, M and Trøseid, M and Laudes, M and Lieb, W and Karlsen, TH and Bang, C and Schramm, C and Franke, A and Hov, JR},
title = {Altered gut microbial metabolism of essential nutrients in primary sclerosing cholangitis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2020.12.058},
pmid = {33387530},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: To influence host and disease phenotype, compositional microbiome changes, which have been demonstrated in patients with primary sclerosing cholangitis (PSC), must be accompanied by functional changes. We therefore aimed to characterize the genetic potential of the gut microbiome in PSC compared to healthy controls (HCs) and inflammatory bowel disease (IBD).<br><br>METHODS: Fecal DNA from two cohorts (one Norwegian and one German), in total comprising 136 patients with PSC (58% with IBD), 158 HCs and 93 IBD patients without PSC were subjected to metagenomic shotgun sequencing, generating 17 billion paired end sequences, which were processed using HUMAnN2 and MetaPhlAn2, and analyzed using generalized linear models and random effects meta-analyses.<br><br>RESULTS: PSC patients had fewer microbial genes compared to HC (P<.0001). Compared to HC, PSC patients showed enrichment and increased prevalence of Clostridium species, and a depletion of e.g., Eubacterium spp. and Ruminococcus obeum. Patients with PSC showed marked differences in the abundance of genes related to vitamin B6 synthesis and branched chain amino acid (BCAA) synthesis (Qfdr<.05). Targeted metabolomics of plasma from an independent set of PSC patients and controls found reduced concentrations of vitamin B6 and BCAAs in PSC (P<.0001), which strongly associated with reduced liver transplantation-free survival (log-rank P<.001). No taxonomic or functional differences were detected between PSC patients with and without IBD.<br><br>CONCLUSION: The gut microbiome of PSC patients exhibits large functional differences compared to HC, including microbial metabolism of essential nutrients. Alterations in related circulating metabolites associated with disease course, suggesting that microbial functions may be relevant for the disease process in PSC.},
}
@article {pmid33387519,
year = {2020},
author = {Mehtani, R and Roy, A and Singh, V},
title = {Gut microbial metagenomics in ACLF: The causality-association conundrum.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2020.12.055},
pmid = {33387519},
issn = {1528-0012},
}
@article {pmid33386517,
year = {2021},
author = {Ray, P and Pandey, U and Das, D and Aich, P},
title = {Vancomycin-Induced Changes in Host Immunity and Behavior: Comparative Genomic and Metagenomic Analysis in C57BL/6 and BALB/c Mice.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {33386517},
issn = {1573-2568},
abstract = {BACKGROUND: The consequence of treatment with antibiotics on the gut microbiota can be destructive. The antibiotics, however, can be utilized to understand the role of gut microbiota on the host physiology.<br><br>AIM: Earlier, we reported the efficacy of vancomycin in gut microbiota perturbation. We continued to understand the effect of restoration kinetics of perturbed gut microbiota on the immunity and behavior of Th1 (C57BL/6)- and Th2 (BALB/c)-biased mice.<br><br>METHODS: We studied restoration kinetics of the gut microbiota for two months following the withdrawal of vancomycin treatment in both mice strains. We analyzed cecal microbiome composition, different behavioral assays, and expression of select genes associated with stress and barrier function in gut and brain.<br><br>RESULTS: Metagenomic analysis of gut microbiota revealed that the treatment with vancomycin caused a significant decrease in the relative abundance of Firmicutes and Bacteroidetes phyla with a time-dependent increase in Proteobacteria and Verrucomicrobia phyla. Maximum restoration (> 70%) of gut microbiota happened by the 15th day of withdrawal of vancomycin. BALB/c mice showed a more efficient restoration of gut microbiota compared to C57BL/6 mice. We established the correlation patterns of gut microbiota alteration and its effect on (a) the behavior of mice, (b) expression of key brain molecules, and (c) immunity-related genes.<br><br>CONCLUSIONS: The results revealed that the gut microbiome profiling, behavior, and immune responses varied significantly between Th1- and Th2-biased mice. By withdrawing the treatment with vancomycin of major gut microbes, important physiological and behavioral changes of both mice strains returned to the normal (untreated control) level.},
}
@article {pmid33386513,
year = {2021},
author = {Zhang, R and Zhang, Q and Yu, G and Zhang, Z},
title = {Metagenomic deep sequencing obtains taxonomic and functional profiles of Haemaphysalis longicornis that vary in response to different developmental stages and sexes.},
journal = {Experimental &amp; applied acarology},
volume = {},
number = {},
pages = {},
pmid = {33386513},
issn = {1572-9702},
support = {2017GSF221017//Development Plan Project of Shandong Province Science and Technology/ ; },
abstract = {Ticks can transmit numerous pathogens and harbor diverse microbial communities. Considerable progress has been made in the characterization of the bacterial profiles of ticks, whereas other members of tick microbiota (such as fungi and viruses) and the functional characteristics of ticks warrant further exploration. To investigate the taxonomic and functional profiles and explore potential pathogens they were carrying, samples of different developmental stages and of both sexes of Haemaphysalis longicornis were collected in the present study and the metagenomic deep sequencing method was applied. Metagenomic deep sequencing results revealed that bacteria were predominant, followed by fungi, viruses, archaea and metazoans. Proteobacteria was the dominant phylum in the microbiota of H. longicornis. The abundance of microbial species varied significantly among groups, the bacteria of nymphs and female adults demonstrated unique characteristics, and the microbial community of males overlapped with those of nymphs and females. Functional annotation results demonstrated that the metagenomic sequences of the three groups were classified under metabolism, genetic information processing, environmental information processing and cellular processes. Differences in functional characteristics were observed in both the pathways composition and abundance of carbohydrate-active enzymes. Furthermore, whole metagenome sequencing helped to elucidate the diversity of pathogens carried by H. longicornis, which may facilitate further research attempting to prevent and control tick-borne diseases.},
}
@article {pmid33385921,
year = {2020},
author = {Chen, H and Liu, C and Teng, Y and Zhang, Z and Chen, Y and Yang, Y},
title = {Environmental risk characterization and ecological process determination of bacterial antibiotic resistome in lake sediments.},
journal = {Environment international},
volume = {147},
number = {},
pages = {106345},
doi = {10.1016/j.envint.2020.106345},
pmid = {33385921},
issn = {1873-6750},
abstract = {The increasing prevalence of antibiotic resistance genes (ARGs) in aquatic environments has attracted considerable concerns due to their potential threat to public health. For reducing environmental risk of ARGs, it is crucial to identify the pathogenic resistant bacteria, determine the driving forces governing the ARG community and apportion their sources, which is yet remained to explore. In this study, we developed a framework integrating high-throughput sequencing (HTS) analyses, null-model-based methods and machine-learning classification tool for understanding the environmental resistome risk and the ecological processes that control the ARG profile in aquatic sediments, and applied to two urban lakes (Lake Tai and Lake Baiyang) in China. The HTS-based metagenomic analyses revealed abundant and diverse resistome, mobilome and virulome in the two lakes, including some emerging ARGs such as mcr and carbapenemases types. Relatively, the diversities for ARGs, mobile genetic elements (MGEs) and virulence factor genes in Lake Baiyang were significantly higher than those in Lake Tai (p < 0.05). The metagenomic assembly and binning approaches tracked a number of potential pathogenic antibiotic resistant bacteria and found the co-occurrence of ARGs, MGEs and human bacterial pathogens in ~50% of the sediment samples, indicating a substantial resistome risk in the lakes. Comparison of multiple-site beta-diversity dissimilarity indexes suggested the ARG diversity was mainly explained by the spatial turnover rather than nestedness and exhibited significant distance-decay pattern. The results of using a novel null-model-based stochasticity ratio showed the stochastic processes made a higher contribution than the deterministic processes on the ARG profile in the environment, especially for Lake Baiyang (>65%). This was confirmed by the determination analyses of various ecological processes on ARG community by utilizing the null-model-based statistical framework for quantifying community assembly. That is, homogenizing dispersal (40%) dominated in Lake Baiyang, followed by homogeneous selection (32%) and ecological drift (15%), while ecological drift (33%) and homogenizing dispersal (31%) were the dominators in Lake Baiyang. SourceTracker analysis showed human sewage-associated sources were the largest contributor (~62%) of ARGs in the environment. The findings shed light on the dissemination risk and driver dynamics of antimicrobial resistance in the aquatic environment, which may help to make effective management strategies for controlling pollution of ARGs.},
}
@article {pmid33385834,
year = {2020},
author = {Kim, N and Ahn, Y and Jo, J and Pyo, H and Lee, J and Choi, J},
title = {Soil assessment after chemical accidents using metabolic profiling and microbial community evaluation.},
journal = {Chemosphere},
volume = {268},
number = {},
pages = {129362},
doi = {10.1016/j.chemosphere.2020.129362},
pmid = {33385834},
issn = {1879-1298},
abstract = {This study investigated the effects of accidental contamination of soils with phenol, toluene, nitric acid, and hydrogen fluoride (HF) by simulating chemical leakage in the soil with/without rain and characterizing the resulting metabolites and microbial. In the case of acid leakage, pH and cation exchange capacity were decreased, and the content of fluoride ion was increased in case of HF leakage. Using mass spectrometry-based metabolomics analysis, phytosphingosine was detected as a distinguishing metabolite in soils contaminated with phenol and HF in rain conditions. Microbial communities were identified by 16s rRNA metagenome sequencing. Sphingomonas was one of the dominant species in soils contaminated with phenol and HF. These results suggest that phytosphingosine and Sphingomonas might be used as biomarkers to evaluate the status of soils contaminated with phenol or HF. Under simulated rain conditions, the species alpha-diversity index of soil microbes and the physicochemical properties of the soil indicated values close to those of the uncontaminated soil. Rain played an important role in the recovery of microbial and metabolic profiles after chemical accidents. Metabolic profiling and microbial community analysis can serve as a diagnostic tool for ecotoxicological research at chemical accident sites.},
}
@article {pmid33385807,
year = {2020},
author = {Makowska, N and Bresa, K and Koczura, R and Philips, A and Nowis, K and Mokracka, J},
title = {Urban wastewater as a conduit for pathogenic Gram-positive bacteria and genes encoding resistance to β-lactams and glycopeptides.},
journal = {The Science of the total environment},
volume = {765},
number = {},
pages = {144176},
doi = {10.1016/j.scitotenv.2020.144176},
pmid = {33385807},
issn = {1879-1026},
abstract = {The emergence and spread of clinical pathogens, antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment pose a direct threat to human and animal health worldwide. In this study, we analyzed qualitatively and quantitatively urban sewage resistome for the occurrence of genes encoding resistance to β-lactams and glycopeptides in the genomes of culturable bacteria, as well as in the wastewater metagenome of the Central Wastewater Treatment Plant in Koziegłowy (Poland). Moreover, we estimated the presence of pathogenic Gram-positive bacteria in wastewater based on analysis of species-specific virulence genes in the wastewater metagenome. The results show that the final effluent contains alarm pathogens with particularly dangerous mechanisms of antibiotic resistance, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). We also noticed that during the wastewater treatment, there is an increase in the frequency of MRSA and VRE. Furthermore, the results prove the effective removal of vanA, but at the same time show that wastewater treatment increases the relative abundance of mecA and virulence genes (groES and sec), indicating the presence of clinical pathogens E. faecalis and S. aureus in the effluent released to surface waters. We also observed an increase in the relative abundance of mecA and vanA genes already in the aeration tank, which suggests accumulation of contaminants affecting enhanced selection and HGT processes in the activated sludge. Moreover, we found a relation between the taxonomic composition and the copy number of ARGs as well as the presence of pathogens at various stages of wastewater treatment. The presence of clinically relevant pathogens, ARB, including multi-resistant bacteria, and ARGs in the effluent indicates that wastewater treatment plant play a key role in the existence of pathogens and antimicrobial resistance spreading pathway in the environment and human communities, which is a direct threat to public health and environmental protection.},
}
@article {pmid33384967,
year = {2020},
author = {Zhao, F and Dong, T and Yuan, KY and Wang, NJ and Xia, FZ and Liu, D and Wang, ZM and Ma, R and Lu, YL and Huang, ZW},
title = {Shifts in the Bacterial Community of Supragingival Plaque Associated With Metabolic-Associated Fatty Liver Disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {581888},
pmid = {33384967},
issn = {2235-2988},
abstract = {Metabolic-associated fatty liver disease (MAFLD), also known as the hepatic manifestation of metabolic disorders, has become one of the most common chronic liver diseases worldwide. The associations between some oral resident microbes and MAFLD have been described. However, changes to the oral microbial community in patients with MAFLD remain unknown. In this study, variations to the supragingival microbiota of MAFLD patients were identified. The microbial genetic profile of supragingival plaque samples from 24 MAFLD patients and 22 healthy participants were analyzed by 16S rDNA sequencing and bioinformatics analysis. Clinical variables, including indicators of insulin resistance, obesity, blood lipids, and hepatocellular damage, were evaluated with laboratory tests and physical examinations. The results showed that the diversity of the supragingival microbiota in MAFLD patients was significantly higher than that in healthy individuals. Weighted UniFrac principal coordinates analysis and partial least squares discriminant analysis showed that the samples from the MAFLD and control groups formed separate clusters (Adonis, P = 0.0120). There were 27 taxa with differential distributions (linear discriminant analysis, LDA>2.0) between two groups, among which Actinomyces spp. and Prevotella 2 spp. were over-represented in the MAFLD group with highest LDA score, while Neisseria spp. and Bergeyella spp. were more abundant in the control group. Co-occurrence networks of the top 50 abundant genera in the two groups suggested that the inter-genera relationships were also altered in the supragingival plaque of MAFLD patients. In addition, in genus level, as risk factors for the development of MAFLD, insulin resistance was positively correlated with the abundances of Granulicatella, Veillonella, Streptococcus, and Scardovia, while obesity was positively correlated to the abundances of Streptococcus, Oslenella, Scardovia, and Selenomonas. Metagenomic predictions based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States revealed that pathways related to sugar (mainly free sugar) metabolism were enriched in the supragingival plaque of the MAFLD group. In conclusion, as compared to healthy individuals, component and interactional dysbioses were observed in the supragingival microbiota of the MAFLD group.},
}
@article {pmid33384902,
year = {2020},
author = {Santos-Júnior, CD and Pan, S and Zhao, XM and Coelho, LP},
title = {Macrel: antimicrobial peptide screening in genomes and metagenomes.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e10555},
pmid = {33384902},
issn = {2167-8359},
abstract = {Motivation: Antimicrobial peptides (AMPs) have the potential to tackle multidrug-resistant pathogens in both clinical and non-clinical contexts. The recent growth in the availability of genomes and metagenomes provides an opportunity for in silico prediction of novel AMP molecules. However, due to the small size of these peptides, standard gene prospection methods cannot be applied in this domain and alternative approaches are necessary. In particular, standard gene prediction methods have low precision for short peptides, and functional classification by homology results in low recall.<br><br>Results: Here, we present Macrel (for metagenomic AMP classification and retrieval), which is an end-to-end pipeline for the prospection of high-quality AMP candidates from (meta)genomes. For this, we introduce a novel set of 22 peptide features. These were used to build classifiers which perform similarly to the state-of-the-art in the prediction of both antimicrobial and hemolytic activity of peptides, but with enhanced precision (using standard benchmarks as well as a stricter testing regime). We demonstrate that Macrel recovers high-quality AMP candidates using realistic simulations and real data.<br><br>Availability: Macrel is implemented in Python 3. It is available as open source at https://github.com/BigDataBiology/macrel and through bioconda. Classification of peptides or prediction of AMPs in contigs can also be performed on the webserver: https://big-data-biology.org/software/macrel.},
}
@article {pmid33384459,
year = {2020},
author = {Tóth, AG and Csabai, I and Maróti, G and Jerzsele, Á and Dubecz, A and Patai, ÁV and Judge, MF and Nagy, SÁ and Makrai, L and Bányai, K and Szita, G and Solymosi, N},
title = {A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {22458},
pmid = {33384459},
issn = {2045-2322},
abstract = {Antimicrobial resistance (AMR) is a global threat gaining more and more practical significance every year. The main determinants of AMR are the antimicrobial resistance genes (ARGs). Since bacteria can share genetic components via horizontal gene transfer, even non-pathogenic bacteria may provide ARG to any pathogens which they become physically close to (e.g. in the human gut). In addition, fermented food naturally contains bacteria in high amounts. In this study, we examined the diversity of ARG content in various kefir and yoghurt samples (products, grains, bacterial strains) using a unified metagenomic approach. We found numerous ARGs of commonly used fermenting bacteria. Even with the strictest filter restrictions, we identified ARGs undermining the efficacy of aminocoumarins, aminoglycosides, carbapenems, cephalosporins, cephamycins, diaminopyrimidines, elfamycins, fluoroquinolones, fosfomycins, glycylcyclines, lincosamides, macrolides, monobactams, nitrofurans, nitroimidazoles, penams, penems, peptides, phenicols, rifamycins, tetracyclines and triclosan. In the case of gene lmrD, we detected genetic environment providing mobility of this ARG. Our findings support the theory that during the fermentation process, the ARG content of foods can grow due to bacterial multiplication. The results presented suggest that the starting culture strains of fermented foods should be monitored and selected in order to decrease the intake of ARGs via foods.},
}
@article {pmid33383910,
year = {2020},
author = {Safaei, N and Mast, Y and Steinert, M and Huber, K and Bunk, B and Wink, J},
title = {Angucycline-like Aromatic Polyketide from a Novel Streptomyces Species Reveals Freshwater Snail Physa acuta as Underexplored Reservoir for Antibiotic-Producing Actinomycetes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {10},
number = {1},
pages = {},
doi = {10.3390/antibiotics10010022},
pmid = {33383910},
issn = {2079-6382},
abstract = {Antibiotic producers have mainly been isolated from soil, which often has led to the rediscovery of known compounds. In this study, we identified the freshwater snail Physa acuta as an unexplored source for new antibiotic producers. The bacterial diversity associated with the snail was characterized by a metagenomic approach using cultivation-independent high-throughput sequencing. Although Actinobacteria represented only 2% of the bacterial community, the focus was laid on the isolation of the genus Streptomyces due to its potential to produce antibiotics. Three Streptomyces strains (7NS1, 7NS2 and 7NS3) were isolated from P. acuta, and the antimicrobial activity of the crude extracts were tested against a selection of Gram-positive and Gram-negative bacteria and fungi. 7NS3 showed the strongest activity against Gram-positive bacteria and, thus, was selected for genome sequencing and a phylogenomic analysis. 7NS3 represents a novel Streptomyces species, which was deposited as Streptomyces sp. DSM 110735 at the Leibniz Institute-German Collection of Microorganisms and Cell Cultures (DSMZ). Bioassay-guided high-performance liquid chromatography (HPLC) and high-resolution electrospray ionization-mass spectrometry (HR-ESI-MS) analyses of crude extract fractions resulted in the detection of four compounds, one of which matched the compound characteristics of emycin A, an angucycline-like aromatic polyketide. Genome mining studies based on the whole-genome sequence of 7NS3 resulted in the identification of a gene cluster potentially coding for emycin A biosynthesis. Our study demonstrates that freshwater snails like P. acuta can represent promising reservoirs for the isolation of new antibiotic-producing actinobacterial species.},
}
@article {pmid33383358,
year = {2020},
author = {Jiang, X and Yan, Y and Feng, L and Wang, F and Guo, Y and Zhang, X and Zhang, Z},
title = {Bisphenol A alters volatile fatty acids accumulation during sludge anaerobic fermentation by affecting amino acid metabolism, material transport and carbohydrate-active enzymes.},
journal = {Bioresource technology},
volume = {323},
number = {},
pages = {124588},
doi = {10.1016/j.biortech.2020.124588},
pmid = {33383358},
issn = {1873-2976},
abstract = {Bisphenol A (BPA), a typical persistent organic pollutant in waste activated sludge, was chosen to explore its influence on the accumulation of volatile fatty acids (VFAs), which is an important raw material, during anaerobic fermentation. BPA in the range of 0-200 mg/kg dry sludge was beneficial to VFAs production, from 1564 mg chemical oxygen demand (COD)/L in the control to 2095 mg COD/L with 50 mg/kg BPA; the acetic acid yield was 563 and 1010 mg COD/L with 0 and 50 mg/kg BPA, respectively. The abundance of microorganisms that can consume VFAs was reduced and those responsible for producing VFAs was increased by BPA. Homologous genes of related enzymes in the pathways for amino acid metabolism, fatty acid biosynthesis, ABC transporters and quorum sensing were enhanced in the presence of BPA. The abundance of carbohydrate-active enzymes increased with BPA when compared with the control, benefitting VFAs production.},
}
@article {pmid33382948,
year = {2021},
author = {Liu, W and Sun, Z and Ma, C and Zhang, J and Ma, C and Zhao, Y and Wei, H and Huang, S and Zhang, H},
title = {Exposure to soil environments during earlier life stages is distinguishable in the gut microbiome of adult mice.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1-13},
doi = {10.1080/19490976.2020.1830699},
pmid = {33382948},
issn = {1949-0984},
abstract = {Environmental exposure during earlier life stages can govern the assembly and development of gut microbiota, yet it is insufficiently understood. In this study, ex-germ-free mice were cohoused with distinct soil-microbiota (from desert, steppe, and forest) beddings within 60 days after birth and subsequently transferred to new soil beddings from 60 to 90th day. Using metagenomic shotgun sequencing, firstly, we found soil microbes from natural environments (birthplace) greatly influenced the gut community assembly in the housing experiment. About 27% microbial species and 12% functional components that associated with birthplaces at Day 60 were still discriminatory of birthplaces after transferring mice to new environments. Moreover, prior soil-exposure types are associated with the magnitude of temporal microbiome change due to environmental shifts. The appropriate soil-exposure (e.g., steppe) might help mice gut microbiome adapt to changing environments or host development. Our study demonstrated the continuous soil-exposure history earlier is associated with the gut microbiome individuality and development later.},
}
@article {pmid33381966,
year = {2020},
author = {Yu, Z and Schwarz, C and Zhu, L and Chen, L and Shen, Y and Yu, P},
title = {Hitchhiking Behavior in Bacteriophages Facilitates Phage Infection and Enhances Carrier Bacteria Colonization.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.0c06969},
pmid = {33381966},
issn = {1520-5851},
abstract = {Interactions between bacteriophages (phages) and biofilms remain poorly understood despite the broad implications for microbial ecology, water quality, and microbiome engineering. Here, we demonstrate that lytic coliphage PHH01 can hitchhike on carrier bacteria Bacillus cereus to facilitate its infection of host bacteria, Escherichia coli, in biofilms. Specifically, PHH01 could adsorb onto the flagella of B. cereus, and thus phage motility was increased, resulting in 4.36-fold more effective infection of E. coli in biofilm relative to free PHH01 alone. Moreover, phage infection mitigated interspecies competition and enhanced B. cereus colonization; the fraction of B. cereus in the final biofilm increased from 9% without phages to 43% with phages. The mutualistic relationship between the coliphage and carrier bacteria was substantiated by migration tests on an E. coli lawn: the conjugation of PHH01 and B. cereus enhanced B. cereus colonization by 6.54-fold compared to B. cereus alone (6.15 vs 0.94 cm2 in 24 h) and PHH01 migration by 5.15-fold compared to PHH01 alone (10.3 vs 2.0 mm in 24 h). Metagenomic and electron microscopic analysis revealed that the phages of diverse taxonomies and different morphologies could be adsorbed by the flagella of B. cereus, suggesting hitchhiking on flagellated bacteria might be a widespread strategy in aquatic phage populations. Overall, our study highlights that hitchhiking behavior in phages can facilitate phage infection of biofilm bacteria, promote carrier bacteria colonization, and thus significantly influence biofilm composition, which holds promise for mediating biofilm functions and moderating associated risks.},
}
@article {pmid33381850,
year = {2020},
author = {Bazin, A and Gautreau, G and Médigue, C and Vallenet, D and Calteau, A},
title = {panRGP: a pangenome-based method to predict genomic islands and explore their diversity.},
journal = {Bioinformatics (Oxford, England)},
volume = {36},
number = {Supplement_2},
pages = {i651-i658},
doi = {10.1093/bioinformatics/btaa792},
pmid = {33381850},
issn = {1367-4811},
abstract = {MOTIVATION: Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity.<br><br>RESULTS: We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on metagenome assembled genomes by redefining the borders of the leuX tRNA hotspot, a well-studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies.<br><br>The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.},
}
@article {pmid33381306,
year = {2020},
author = {Pace, J and Youens-Clark, K and Freeman, C and Hurwitz, B and Van Doorslaer, K},
title = {PuMA: A papillomavirus genome annotation tool.},
journal = {Virus evolution},
volume = {6},
number = {2},
pages = {veaa068},
pmid = {33381306},
issn = {2057-1577},
abstract = {High-throughput sequencing technologies provide unprecedented power to identify novel viruses from a wide variety of (environmental) samples. The field of 'viral metagenomics' has dramatically expanded our understanding of viral diversity. Viral metagenomic approaches imply that many novel viruses will not be described by researchers who are experts on (the genomic organization of) that virus family. We have developed the papillomavirus annotation tool (PuMA) to provide researchers with a convenient and reproducible method to annotate and report novel papillomaviruses. PuMA currently correctly annotates 99% of the papillomavirus genes when benchmarked against the 655 reference genomes in the papillomavirus episteme. Compared to another viral annotation pipeline, PuMA annotates more viral features while being more accurate. To demonstrate its general applicability, we also developed a preliminary version of PuMA that can annotate polyomaviruses. PuMA is available on GitHub (https://github.com/KVD-lab/puma) and through the iMicrobe online environment (https://www.imicrobe.us/#/apps/puma).},
}
@article {pmid33381096,
year = {2020},
author = {Napieralski, SA and Roden, EE},
title = {The Weathering Microbiome of an Outcropping Granodiorite.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {601907},
pmid = {33381096},
issn = {1664-302X},
abstract = {Microorganisms have long been recognized for their capacity to catalyze the weathering of silicate minerals. While the vast majority of studies on microbially mediated silicate weathering focus on organotrophic metabolism linked to nutrient acquisition, it has been recently demonstrated that chemolithotrophic ferrous iron [Fe(II)] oxidizing bacteria (FeOB) are capable of coupling the oxidation of silicate mineral Fe(II) to metabolic energy generation and cellular growth. In natural systems, complex microbial consortia with diverse metabolic capabilities can exist and interact to influence the biogeochemical cycling of essential elements, including iron. Here we combine microbiological and metagenomic analyses to investigate the potential interactions among metabolically diverse microorganisms in the near surface weathering of an outcrop of the Rio Blanco Quartz Diorite (DIO) in the Luquillo Mountains of Puerto Rico. Laboratory based incubations utilizing ground DIO as metabolic energy source for chemolithotrophic FeOB confirmed the ability of FeOB to grow via the oxidation of silicate-bound Fe(II). Dramatically accelerated rates of Fe(II)-oxidation were associated with an enrichment in microorganisms with the genetic capacity for iron oxidizing extracellular electron transfer (EET) pathways. Microbially oxidized DIO displayed an enhanced susceptibility to the weathering activity of organotrophic microorganisms compared to unoxidized mineral suspensions. Our results suggest that chemolithotrophic and organotrophic microorganisms are likely to coexist and contribute synergistically to the overall weathering of the in situ bedrock outcrop.},
}
@article {pmid33381092,
year = {2020},
author = {Qian, L and Shi, Y and Li, F and Wang, Y and Ma, M and Zhang, Y and Shao, YW and Zheng, G and Zhang, G},
title = {Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of External Ventricular and Lumbar Drainage-Associated Ventriculitis and Meningitis.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {596175},
pmid = {33381092},
issn = {1664-302X},
abstract = {Metagenomic next-generation sequencing (mNGS) has become a widely used technology that can accurately detect individual pathogens. This prospective study was performed between February 2019 and September 2019 in one of the largest clinical neurosurgery centers in China. The study aimed to evaluate the performance of mNGS on cerebrospinal fluid (CSF) from neurosurgical patients for the diagnosis of external ventricular and lumbar drainage (EVD/LD)-associated ventriculitis and meningitis (VM). We collected CSF specimens from neurosurgical patients with EVD/LD for more than 24 h to perform conventional microbiological studies and mNGS analyses in a pairwise manner. We also investigated the usefulness of mNGS of CSF for the diagnosis of EVD/LD-associated VM. In total, 102 patients were enrolled in this study and divided into three groups, including confirmed VM (cVM) (39), suspected VM (sVM) (49), and non-VM (nVM) (14) groups. Of all the patients, mNGS detected 21 Gram-positive bacteria, 20 Gram-negative bacteria, and five fungi. The three primary bacteria detected were Staphylococcus epidermidis (9), Acinetobacter baumannii (5), and Staphylococcus aureus (3). The mNGS-positive coincidence rate of confirmed EVD/LD-associated VM was 61.54% (24/39), and the negative coincidence rate of the nVM group was 100% (14/14). Of 15 VM pathogens not identified by mNGS in the cVM group, eight were negative with mNGS and seven were inconsistent with the conventional microbiological identification results. In addition, mNGS identified pathogens in 22 cases that were negative using conventional methods; of them, 10 patients received a favorable clinical treatment; thus, showing the benefit of mNGS-guided therapy.},
}
@article {pmid33380742,
year = {2020},
author = {Marshall, JR and Yao, P and Montgomery, SL and Finnigan, JD and Thorpe, TW and Palmer, RB and Mangas-Sanchez, J and Duncan, RAM and Heath, RS and Graham, KM and Cook, DJ and Charnock, SJ and Turner, NJ},
title = {Screening and characterization of a diverse panel of metagenomic imine reductases for biocatalytic reductive amination.},
journal = {Nature chemistry},
volume = {},
number = {},
pages = {},
pmid = {33380742},
issn = {1755-4349},
abstract = {Finding faster and simpler ways to screen protein sequence space to enable the identification of new biocatalysts for asymmetric synthesis remains both a challenge and a rate-limiting step in enzyme discovery. Biocatalytic strategies for the synthesis of chiral amines are increasingly attractive and include enzymatic asymmetric reductive amination, which offers an efficient route to many of these high-value compounds. Here we report the discovery of over 300 new imine reductases and the production of a large (384 enzymes) and sequence-diverse panel of imine reductases available for screening. We also report the development of a facile high-throughput screen to interrogate their activity. Through this approach we identified imine reductase biocatalysts capable of accepting structurally demanding ketones and amines, which include the preparative synthesis of N-substituted β-amino ester derivatives via a dynamic kinetic resolution process, with excellent yields and stereochemical purities.},
}
@article {pmid33380558,
year = {2021},
author = {Choi, SI and Son, JH and Kim, N and Kim, YS and Nam, RH and Park, JH and Song, CH and Yu, JE and Lee, DH and Yoon, K and Min, H and Kim, YR and Seok, YJ},
title = {Changes in Cecal Microbiota and Short-chain Fatty Acid During Lifespan of the Rat.},
journal = {Journal of neurogastroenterology and motility},
volume = {27},
number = {1},
pages = {134-146},
doi = {10.5056/jnm20148},
pmid = {33380558},
issn = {2093-0879},
abstract = {Background/Aims: The gut microbiota regulates intestinal immune homeostasis through host-microbiota interactions. Multiple factors affect the gut microbiota, including age, sex, diet, and use of drugs. In addition, information on gut microbiota differs depending on the samples. The aim of this study is to investigate whether changes in cecal microbiota depend on aging.<br><br>Methods: Gut microbiota in cecal contents of 6-, 31-, and 74-week-old and 2-year-old male Fischer-344 rats (corresponding to 5-, 30-, 60-, and 80-year-old humans in terms of age) were analyzed using 16S ribosomal RNA metagenome sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) based on the Kyoto Encyclopedia of Genes and Genomes orthology. Moreover, short-chain fatty acid (SCFA) level in cecum and inflammation related factors were measured using real-time quantitative polymerase chain reaction and enzyme linked immunosorbent assay.<br><br>Results: Alpha and beta diversity did not change significantly with age. At the family level, Lachnospiraceae and Ruminococcaceae, which produce SCFAs, showed significant change in 31-week-old rats: Lachnospiraceae significantly increased at 31 weeks of age, compared to other age groups, while Ruminococcaceae decreased. Butyrate levels in cecum were significantly increased in 31-week-old rats, and the expression of inflammation related genes was increased followed aging. Especially, EU622775_s and EU622773_s, which were highly abundance species in 31-week-old rats, showed significant relationship with butyrate concentration. Enzymes required for producing butyrate-acetyl-CoA transferase, butyryl-CoA dehydrogenase, and butyrate kinase-were not predicted by PICRUSt.<br><br>Conclusions: Major bacterial taxa in the cecal lumen, such as Lachnospiraceae, well-known SCFAs-producing family, changed in 31-week-old rats. Moreover, unknown species EU622775_s and EU622773_s showed strong association with cecal butyrate level at 31 weeks of age.},
}
@article {pmid33380187,
year = {2021},
author = {Fang, X and Cai, Y and Mei, J and Huang, Z and Zhang, C and Yang, B and Li, W and Zhang, W},
title = {Optimizing culture methods according to preoperative mNGS results can improve joint infection diagnosis.},
journal = {The bone &amp; joint journal},
volume = {103-B},
number = {1},
pages = {39-45},
doi = {10.1302/0301-620X.103B1.BJJ-2020-0771.R2},
pmid = {33380187},
issn = {2049-4408},
abstract = {AIMS: Metagenomic next-generation sequencing (mNGS) is useful in the diagnosis of infectious disease. However, while it is highly sensitive at identifying bacteria, it does not provide information on the sensitivity of the organisms to antibiotics. The purpose of this study was to determine whether the results of mNGS can be used to guide optimization of culture methods to improve the sensitivity of culture from intraoperative samples.<br><br>METHODS: Between July 2014 and October 2019, patients with suspected joint infection (JI) from whom synovial fluid (SF) was obtained preoperatively were enrolled. Preoperative aspirated SF was analyzed by conventional microbial culture and mNGS. In addition to samples taken for conventional microbial culture, some samples were taken for intraoperative culture to optimize the culture method according to the preoperative mNGS results. The demographic characteristics, medical history, laboratory examination, mNGS, and culture results of the patients were recorded, and the possibility of the optimized culture methods improving diagnostic efficiency was evaluated.<br><br>RESULTS: A total of 56 cases were included in this study. There were 35 cases of JI and 21 cases of non-joint infection (NJI). The sensitivity, specificity, and accuracy of intraoperative microbial culture after optimization of the culture method were 94.29%, 76.19%, and 87.5%, respectively, while those of the conventional microbial culture method were 60%, 80.95%, and 67.86%, respectively.<br><br>CONCLUSION: Preoperative aspirated SF detected via mNGS can provide more aetiological information than preoperative culture, which can guide the optimization and improve the sensitivity of intraoperative culture. Cite this article: Bone Joint J 2021;103-B(1):39-45.},
}
@article {pmid33379234,
year = {2020},
author = {Eberhardt, MF and Irazoqui, JM and Amadio, AF},
title = {β-Galactosidases from a Sequence-Based Metagenome: Cloning, Expression, Purification and Characterization.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/microorganisms9010055},
pmid = {33379234},
issn = {2076-2607},
support = {PNBIO1131033//Instituto Nacional de Tecnología Agropecuaria (INTA)/ ; PNBIO1130033//Instituto Nacional de Tecnología Agropecuaria (INTA)/ ; PICT2017-0191//Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación/ ; IO-2017-0172//Agencia Santafesina de Ciencia Tecnología e Innovación/ ; },
abstract = {Stabilization ponds are a common treatment technology for wastewater generated by dairy industries. Large proportions of cheese whey are thrown into these ponds, creating an environmental problem because of the large volume produced and the high biological and chemical oxygen demands. Due to its composition, mainly lactose and proteins, it can be considered as a raw material for value-added products, through physicochemical or enzymatic treatments. β-Galactosidases (EC 3.2.1.23) are lactose modifying enzymes that can transform lactose in free monomers, glucose and galactose, or galactooligosacharides. Here, the identification of novel genes encoding β-galactosidases, identified via whole-genome shotgun sequencing of the metagenome of dairy industries stabilization ponds is reported. The genes were selected based on the conservation of catalytic domains, comparing against the CAZy database, and focusing on families with β-galactosidases activity (GH1, GH2 and GH42). A total of 394 candidate genes were found, all belonging to bacterial species. From these candidates, 12 were selected to be cloned and expressed. A total of six enzymes were expressed, and five cleaved efficiently ortho-nitrophenyl-β-galactoside and lactose. The activity levels of one of these novel β-galactosidase was higher than other enzymes reported from functional metagenomics screening and higher than the only enzyme reported from sequence-based metagenomics. A group of novel mesophilic β-galactosidases from diary stabilization ponds' metagenomes was successfully identified, cloned and expressed. These novel enzymes provide alternatives for the production of value-added products from dairy industries' by-products.},
}
@article {pmid33378601,
year = {2020},
author = {Faulkner, CL and Luo, YX and Isaacs, S and Rawlinson, WD and Craig, ME and Kim, KW},
title = {The virome in early life and childhood and development of islet autoimmunity and type 1 diabetes: A systematic review and meta-analysis of observational studies.},
journal = {Reviews in medical virology},
volume = {},
number = {},
pages = {e2209},
doi = {10.1002/rmv.2209},
pmid = {33378601},
issn = {1099-1654},
support = {Practitioner fellowship (APP1136735)//National Health and Medical Research Council/ ; Postdoctoral Fellowship (3-PDF-2020-940-A-N)//Juvenile Diabetes Research Foundation International/ ; Lindsey Baudinet Award//Australian Diabetes Society/ ; },
abstract = {Viruses are postulated as primary candidate triggers of islet autoimmunity (IA) and type 1 diabetes (T1D), based on considerable epidemiological and experimental evidence. Recent studies have investigated the association between all viruses (the 'virome') and IA/T1D using metagenomic next-generation sequencing (mNGS). Current associations between the early life virome and the development of IA/T1D were analysed in a systematic review and meta-analysis of human observational studies from Medline and EMBASE (published 2000-June 2020), without language restriction. Inclusion criteria were as follows: cohort and case-control studies examining the virome using mNGS in clinical specimens of children ≤18 years who developed IA/T1D. The National Health and Medical Research Council level of evidence scale and Newcastle-Ottawa scale were used for study appraisal. Meta-analysis for exposure to specific viruses was performed using random-effects models, and the strength of association was measured using odds ratios (ORs) and 95% confidence intervals (CIs). Eligible studies (one case-control, nine nested case-control) included 1,425 participants (695 cases, 730 controls) and examined IA (n = 1,023) or T1D (n = 402). Meta-analysis identified small but significant associations between IA and number of stool samples positive for all enteroviruses (OR 1.14, 95% CI 1.00-1.29, p = 0.05; heterogeneity χ2 = 1.51, p = 0.68, I2 = 0%), consecutive positivity for enteroviruses (1.55, 1.09-2.20, p = 0.01; χ2 = 0.19, p = 0.91, I2 = 0%) and number of stool samples positive specifically for enterovirus B (1.20, 1.01-1.42, p = 0.04; χ2 = 0.03, p = 0.86, I2 = 0%). Virome analyses to date have demonstrated associations between enteroviruses and IA that may be clinically significant. However, larger prospective mNGS studies with more frequent sampling and follow-up from pregnancy are required to further elucidate associations between early virus exposure and IA/T1D.},
}
@article {pmid33378381,
year = {2020},
author = {Laso-Jadart, R and Ambroise, C and Peterlongo, P and Madoui, MA},
title = {metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0244637},
doi = {10.1371/journal.pone.0244637},
pmid = {33378381},
issn = {1932-6203},
abstract = {The availability of large metagenomic data offers great opportunities for the population genomic analysis of uncultured organisms, which represent a large part of the unexplored biosphere and play a key ecological role. However, the majority of these organisms lack a reference genome or transcriptome, which constitutes a technical obstacle for classical population genomic analyses. We introduce the metavariant species (MVS) model, in which a species is represented only by intra-species nucleotide polymorphism. We designed a method combining reference-free variant calling, multiple density-based clustering and maximum-weighted independent set algorithms to cluster intra-species variants into MVSs directly from multisample metagenomic raw reads without a reference genome or read assembly. The frequencies of the MVS variants are then used to compute population genomic statistics such as FST, in order to estimate genomic differentiation between populations and to identify loci under natural selection. The MVS construction was tested on simulated and real metagenomic data. MVSs showed the required quality for robust population genomics and allowed an accurate estimation of genomic differentiation (ΔFST < 0.0001 and <0.03 on simulated and real data respectively). Loci predicted under natural selection on real data were all detected by MVSs. MVSs represent a new paradigm that may simplify and enhance holistic approaches for population genomics and the evolution of microorganisms.},
}
@article {pmid33378284,
year = {2020},
author = {Afolayan, AO and Ayeni, FA},
title = {Metagenomic Analysis of Bacterial Communities in Water and Soil of the Fulani and non-Fulani in Nigeria.},
journal = {Journal of infection in developing countries},
volume = {14},
number = {12},
pages = {},
doi = {10.3855/jidc.12975},
pmid = {33378284},
issn = {1972-2680},
abstract = {INTRODUCTION: Interactions between environmental factors (water and soil) and humans are inevitable, particularly in rural and semi-urbanized regions. As such, knowledge on the microbial constituents of these environmental factors is key to understanding potential risk to public health. However, the microbial profile of soil and water present in vulnerable human communities in Nigeria is currently unknown. This study sought to investigate the composition of soil and water microbiota in the environment inhabited by recently studied human communities (the Fulani nomadic group and the urbanized Jarawa ethnic group) and estimate the contribution of these environmental factors to the microbiome of the aforementioned human communities.<br><br>METHODOLOGY: Soil and water samples were collected from the Fulani and non-Fulani community in Jengre (Plateau State, Nigeria) and Jos (Plateau State, Nigeria), respectively. Genomic DNA was extracted from these environmental samples, followed by Illumina sequencing of the V4 region of the 16S rRNA gene and bioinformatics analysis via Quantitative Insights into Microbial Ecology QIIME.<br><br>RESULTS: There is abundance of Proteobacteria (43%) signature members in soil samples obtained from both human communities. Analysis of the water samples revealed the abundance of Proteobacteria, particularly in water sourced from the borehole (Fulani). Pseudomonas (30%) had higher relative abundance in the drinking water of the Fulani.<br><br>CONCLUSIONS: The drinking water of the Fulani could be a potential health risk to the studied Fulani community. Factors that increase the abundance of public health threats and health risk, such as hygiene practices, soil and water quality need to be studied further for the improvement of health in vulnerable populations.},
}
@article {pmid33376062,
year = {2020},
author = {Brubaker, L and Luu, S and Hoffman, K and Wood, A and Navarro Cagigas, M and Yao, Q and Petrosino, J and Fisher, W and Van Buren, G},
title = {Microbiome changes associated with acute and chronic pancreatitis: A systematic review.},
journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pan.2020.12.013},
pmid = {33376062},
issn = {1424-3911},
abstract = {BACKGROUND: Altered intestinal microbiota has been reported in pancreatic disorders, however, it remains unclear whether these changes alter the course of disease in patients with acute (AP) and chronic pancreatitis (CP), or whether these disease states alter the environment to enable pathogenic microbial composition changes to occur. We undertook a systematic review to characterize the gut microbiome in pancreatitis patients.<br><br>METHODS: MEDLINE and EMBASE were searched for studies on microbiota in pancreatitis published from January 1, 2000 to June 5, 2020. Animal studies, reviews, case reports, and non-English articles were excluded. A frequency analysis was performed for outcomes reported in ≥2 studies and studies were analyzed for risk of bias and quality of evidence.<br><br>RESULTS: 22 papers met inclusion criteria; 15 included AP, 7 included CP. No studies were appropriately designed to assess whether alterations in the gut microbiome exacerbate pancreatitis or develop as a result of pancreatitis. We did identify several patterns of microbiome changes that are associated with pancreatitis. The gut microbiome demonstrated decreased alpha diversity in 3/3 A P studies and 3/3 C P studies. Beta diversity analysis revealed differences in bacterial community composition in the gut microbiome in 2/2 A P studies and 3/3 C P studies. Functionally, gut microbiome changes were associated with infectious pathways in AP and CP. Several studies suffered from high risk of bias and inadequate quality.<br><br>CONCLUSIONS: Detecting differences in microbial composition associated with AP and CP may represent a diagnostic tool. Appropriately controlled longitudinal studies are needed to determine whether microbiome changes are causative or reactive in pancreatitis.},
}
@article {pmid33375982,
year = {2021},
author = {Kalyani, DC and Reichenbach, T and Aspeborg, H and Divne, C},
title = {A homodimeric bacterial exo-β-1,3-glucanase derived from moose rumen microbiome shows a structural framework similar to yeast exo-β-1,3-glucanases.},
journal = {Enzyme and microbial technology},
volume = {143},
number = {},
pages = {109723},
doi = {10.1016/j.enzmictec.2020.109723},
pmid = {33375982},
issn = {1879-0909},
abstract = {The impact of various β-glucans on the gut microbiome and immune system of vertebrates is becoming increasingly recognized. Besides the fundamental interest in understanding how β-glucans support human and animal health, enzymes that metabolize β-glucans are of interest for hemicellulose bioprocessing. Our earlier metagenomic analysis of the moose rumen microbiome identified a gene coding for a bacterial enzyme with a possible role in β-glucan metabolization. Here, we report that the enzyme, mrbExg5, has exo-β-1,3-glucanase activity on β-1,3-linked glucooligosaccharides and laminarin, but not on β-1,6- or β-1,4-glycosidic bonds. Longer oligosaccharides are good substrates, while shorter substrates are readily transglycosylated into longer products. The enzyme belongs to glycoside hydrolase subfamily GH5_44, which is a close phylogenetic neighbor of the subfamily GH5_9 exo-β-1,3-glucanases of the yeasts Saccharomyces cerevisiae and Candida albicans. The crystal structure shows that unlike the eukaryotic relatives, mrbExg5 is a functional homodimer with a binding region characterized by: (i) subsite +1 can accommodate a branched sugar on the β-1,3-glucan backbone; (ii) subsite +2 is restricted to exclude backbone substituents; and (iii) a fourth subsite (+3) formed by a unique loop. mrbExg5 is the first GH5_44 enzyme to be structurally characterized, and the first bacterial GH5 with exo-β-1,3-glucanase activity.},
}
@article {pmid33374130,
year = {2020},
author = {Cozannet, M and Borrel, G and Roussel, E and Moalic, Y and Allioux, M and Sanvoisin, A and Toffin, L and Alain, K},
title = {New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/microorganisms9010030},
pmid = {33374130},
issn = {2076-2607},
support = {-//French Ministry of Higher Education and Research/ ; -//Région Bretagne/ ; ANR-10-LABX-1//LabexMer/ ; -//MERLIN Abyss/ ; IRP 1211//Sino-French Laboratoty MicrobSea/ ; },
abstract = {Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus 'Methanomassiliicoccus armoricus MXMAG1'. Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades ('free-living'/non-host-associated environmental clade and 'host-associated'/digestive clade) allowed us to explore the putative physiological traits of Candidatus 'M. armoricus MXMAG1'. As expected, Ca. 'Methanomassiliicoccus armoricus MXMAG1' had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the 'free-living' clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.},
}
@article {pmid33374068,
year = {2020},
author = {Gao, J and Zhang, SH and Wang, R and Jin, PK},
title = {[Metagenomic Insights into Salinity Build-up in Microbial Communities and Metabolism of Hydrolytic Bioreactor Treating High-color PDWW].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {41},
number = {12},
pages = {5518-5526},
doi = {10.13227/j.hjkx.202005080},
pmid = {33374068},
issn = {0250-3301},
abstract = {In this study, to solve the problem of salinity enrichment in industrial wastewater recycling, a hydrolytic bioreactor was continuously operated to treat high-color printing and dyeing wastewater (PDWW) with salinity build-up. Nearly complete color removal was achieved even with salinity build-ups from 0.5 to 4 g·L-1 in the influent. Pyrosequencing of 16S rRNA genes showed that the salinity build-up results in the decrease of microbial species from 882 to 631; however, the biodiversity of the bacterial community remains stable. Metagenomic analysis indicated that salinity build-up caused no obvious effect on the overall function of the bacterial community, but altered the abundance of specific decoloring genes. Proteobacteria dominated in the bioreactor, and Methanothrix and Geobacter were the dominant genera under low salinity conditions. Proteobacteria increased in abundance with salinity build-up. Desulfovibrio and Desulfococcus were the two predominant genera in the bioreactor fed with sodium sulphate salinity build-up, demonstrating opposite responses to the sodium stress. PICRUSt functional analysis showed that the relative abundance of the decolorizing enzymes SOD1 and SOD2 decreased significantly, but the relative abundance of CAT and TYR increased, ensuring the stability of the decolorizing function of the hydrolysis biological system. From the perspective of the functional genes of hydrolysis decolorization, this study explored the effect of salinity build-up on the microbial community and function of hydrolysis, providing a theoretical basis for the study of decolorization and organic matter removal mechanism of PDWW under the condition of salinity build-up.},
}
@article {pmid33373956,
year = {2020},
author = {Zhang, H and Zhang, Z and Song, J and Cai, L and Yu, Y and Fang, H},
title = {Foam shares antibiotic resistomes and bacterial pathogens with activated sludge in wastewater treatment plants.},
journal = {Journal of hazardous materials},
volume = {408},
number = {},
pages = {124855},
doi = {10.1016/j.jhazmat.2020.124855},
pmid = {33373956},
issn = {1873-3336},
abstract = {Foaming is a common operational problem that occurs in activated sludge (AS) from many wastewater treatment plants (WWTPs), but the characteristic of antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in foams is generally lacking. Here, we used a metagenomic approach to characterize the profile of ARGs and HPB in foams and AS from full-scale WWTPs receiving pesticide wastewater. No significant difference in the microbial communities was noted between the AS and foam samples. The diversity and abundance of ARGs in the foams were similar to those in the pertinent AS samples. Procrustes analysis suggested that the bacterial community is the major driver of ARGs. Metagenomic assembly also indicated that most ARGs (e.g., multidrug, rifamycin, peptides, macrolide-lincosamide-streptogramin, tetracycline, fluoroquinolone, and beta-lactam resistance genes) were carried by chromosomes rather than mobile genetic elements. Moreover, the relative abundances of HPB, Pseudomonas putida and Mycobacterium smegmatis, were enriched in the foam samples. Nine HPB were identified as carriers of 21 ARG subtypes, of which Pseudomonas aeruginosa could carry 12 ARG subtypes. Overall, this study indicates the prevalence of ARGs, HPB, and ARG-carrying HPB in foams, which highlights the potential risk of foams in spreading ARGs and HPB into the surrounding environments.},
}
@article {pmid33373788,
year = {2020},
author = {Du, Q and Mu, Q and Wu, G},
title = {Metagenomic and bioanalytical insights into quorum sensing of methanogens in anaerobic digestion systems with or without the addition of conductive filter.},
journal = {The Science of the total environment},
volume = {763},
number = {},
pages = {144509},
doi = {10.1016/j.scitotenv.2020.144509},
pmid = {33373788},
issn = {1879-1026},
abstract = {Understanding microbial interactions in the methanogenesis system through quorum sensing (QS) is very important for system optimization. Known QS genes were collected and classified into seven groups based on the signal molecules, which were used for constructing a hierarchical quorum sensing database (QSDB). QSDB containing 39,981 QS genes of seven QS groups was constructed and QS genes were analyzed with QSDB. Methanogen genomes were aligned with QSDB and acyl-homoserine lactones (AHLs) system was predicted as the most probable QS system. This database was further applied to analyze QS in methanogens from two upflow anaerobic sludge blanket-anaerobic filter hybrid reactors with conductive filter (CFB) and nonconductive filter (SEP), and a control without filter (CON). The maximum COD degradation rates in CFB (722.2 ± 10.1 mg/L·h) was elevated by 42.9% compared to CON (505.4 ± 5.98 mg/L·h). Metagenomic sequencing revealed Methanosaeta, Methanobacterium, and Methanosarcina were dominant, and the abundances was 4.3 times higher in the sludge of CFB compared to CON. The overall abundance of QS genes was CFB > SEP > CON, and AHLs were the most abundant group of QS genes. The filI/filR system, a luxI/luxR homolog, was firstly detected in methanogens, showing a high abundance in the CFB (0.085%) compared to in the CON (0.058%). The concentration of AHL molecules in CFB biofilms (0.04%) was about four times that in the CON (0.01%). Syntrophobacter and Smithella were the two major syntrophic bacteria of methanogens, and their abundances were positively correlated with methanogens. In addition, Syntrophobacter and Smithella harbored QS RpfB (component of the diffusible signal factor system) and PDE (component of cyclic di-GMP system). This study provides useful guidance for deeply understanding of QS in anaerobic digestion systems.},
}
@article {pmid33373390,
year = {2020},
author = {Hull, JJA and Qi, M and Montmayeur, AM and Kumar, D and Velasquez, DE and Moon, SS and Magaña, LC and Betrapally, N and Ng, TFF and Jiang, B and Marthaler, D},
title = {Metagenomic sequencing generates the whole genomes of porcine rotavirus A, C, and H from the United States.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0244498},
doi = {10.1371/journal.pone.0244498},
pmid = {33373390},
issn = {1932-6203},
abstract = {The genus Rotavirus comprises eight species, designated A to H, and two recently identified tentative species I in dogs and J in bats. Species Rotavirus A, B, C and H (RVA, RVB, RVC and RVH) have been detected in humans and animals. While human and animal RVA are well characterized and defined, complete porcine genome sequences in the GenBank are limited compared to human strains. Here, we used a metagenomic approach to sequence the 11 segments of RVA, RVC and RVH strains from piglets in the United States (US) and explore the evolutionary relations of these RV species. Metagenomics identified Astroviridae, Picornaviridae, Caliciviridae, Coronoviridae in samples MN9.65 and OK5.68 while Picobirnaviridae and Arteriviridae were only identified in sample OK5.68. Whole genome sequencing and phylogenetic analyses identified multiple genotypes with the RVA of strain MN9.65 and OK5.68, with the genome constellation of G5/G9-P[7]/P[13]-I5/I5- R1/R1-C1-M1-A8-N1-T7-E1/E1-H1 and G5/G9-P[6]/P[7]-I5-R1/R1-C1-M1-A8-N1-T1/T7-E1/E1-H1, respectively. The RVA strains had a complex evolutionary relationship with other mammalian strains. The RVC strain OK5.68 had a genome constellation of G9-P[6]-I1-R1-C5-M6-A5-N1-T1-E1-H1, and shared an evolutionary relationship with porcine strains from the US. The RVH strains MN9.65 and OK5.68 had the genome constellation of G5-P1-I1-R1-C1-M1-A5-N1-T1-E4-H1 and G5-P1-I1-R1-C1-M1-A5-N1-T1-E1-H1, indicating multiple RVH genome constellations are circulating in the US. These findings allow us to understand the complexity of the enteric virome, develop improved screening methods for RVC and RVH strains, facilitate expanded rotavirus surveillance in pigs, and increase our understanding of the origin and evolution of rotavirus species.},
}
@article {pmid33372909,
year = {2020},
author = {Fedorov, DE and Olekhnovich, EI and Pavlenko, AV and Klimina, KM and Pokataev, IA and Manolov, AI and Konanov, DN and Veselovsky, VA and Ilina, EN},
title = {[Intestinal microbiome as a predictor of the anti-PD-1 therapy success: metagenomic data analysis].},
journal = {Biomeditsinskaia khimiia},
volume = {66},
number = {6},
pages = {502-507},
doi = {10.18097/PBMC20206606502},
pmid = {33372909},
issn = {2310-6972},
abstract = {Anti-PD-1 immunotherapy has a large impact on cancer treatment but the rate of positive treatment outcomes is 40-45% and depends on many factors. One of the factors affecting the outcome of immunotherapy is the gut microbiota composition. This effect has been demonstrated both in model objects and in clinical patients groups. However, in order to identify clear causal relationships between microbiota and anti-PD1 immunotherapy response, it is necessary to expand the number of patients and experimental samples. This work presents an analysis of metagenomic data obtained using whole-genome sequencing of stool samples from melanoma patients (n=45) with different responses to anti-PD1 therapy. The analysis of the differential representation of microbial species has shown a difference in the composition of the microbiota between the experimental groups. Results of this study indicate existence of a strong link between the composition of the gut microbiota and the outcome of anti-PD1 therapy. Expansion of similar research may help develop additional predictive tools for the outcome of anti-PD1 cancer immunotherapy, as well as increase its effectiveness.},
}
@article {pmid33372654,
year = {2020},
author = {Belcour, A and Frioux, C and Aite, M and Bretaudeau, A and Hildebrand, F and Siegel, A},
title = {Metage2Metabo, microbiota-scale metabolic complementarity for the identication of key species.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
doi = {10.7554/eLife.61968},
pmid = {33372654},
issn = {2050-084X},
support = {Gut Microbes and Health BB/r012490/1,and its constituent project BBS/e/F/000Pr1035//BBSRC/ ; IDEALG (ANR-10-BTBR-04) Investissements d'Avenir//2/ ; },
abstract = {To capture the functional diversity of microbiota, one must identify metabolic functions and species of interest within hundreds or thousands of microorganisms. We present Metage2Metabo (M2M) a resource that meets the need for de-novo functional screening of genome-scale metabolic networks (GSMNs) at the scale of a metagenome, and the identification of critical species with respect to metabolic cooperation. M2M comprises a flexible pipeline for the characterisation of individual metabolisms and collective metabolic complementarity. In addition, M2M identifies key species, that are meaningful members of the community for functions of interest. We demonstrate that M2M is applicable to collections of genomes as well as metagenome-assembled genomes, permits an efficient GSMN reconstruction with Pathway Tools, and assesses the cooperation potential between species. M2M identifies key organisms by reducing the complexity of a large-scale microbiota into minimal communities with equivalent properties, suitable for further analyses.},
}
@article {pmid33372605,
year = {2020},
author = {Li, C and Chen, J and Li, SC},
title = {Deep learning for HGT insertion sites recognition.},
journal = {BMC genomics},
volume = {21},
number = {Suppl 11},
pages = {893},
pmid = {33372605},
issn = {1471-2164},
support = {7005215//City University of Hong Kong/ ; },
abstract = {BACKGROUND: Horizontal Gene Transfer (HGT) refers to the sharing of genetic materials between distant species that are not in a parent-offspring relationship. The HGT insertion sites are important to understand the HGT mechanisms. Recent studies in main agents of HGT, such as transposon and plasmid, demonstrate that insertion sites usually hold specific sequence features. This motivates us to find a method to infer HGT insertion sites according to sequence features.<br><br>RESULTS: In this paper, we propose a deep residual network, DeepHGT, to recognize HGT insertion sites. To train DeepHGT, we extracted about 1.55 million sequence segments as training instances from 262 metagenomic samples, where the ratio between positive instances and negative instances is about 1:1. These segments are randomly partitioned into three subsets: 80% of them as the training set, 10% as the validation set, and the remaining 10% as the test set. The training loss of DeepHGT is 0.4163 and the validation loss is 0.423. On the test set, DeepHGT has achieved the area under curve (AUC) value of 0.8782. Furthermore, in order to further evaluate the generalization of DeepHGT, we constructed an independent test set containing 689,312 sequence segments from another 147 gut metagenomic samples. DeepHGT has achieved the AUC value of 0.8428, which approaches the previous test AUC value. As a comparison, the gradient boosting classifier model implemented in PyFeat achieve an AUC value of 0.694 and 0.686 on the above two test sets, respectively. Furthermore, DeepHGT could learn discriminant sequence features; for example, DeepHGT has learned a sequence pattern of palindromic subsequences as a significantly (P-value=0.0182) local feature. Hence, DeepHGT is a reliable model to recognize the HGT insertion site.<br><br>CONCLUSION: DeepHGT is the first deep learning model that can accurately recognize HGT insertion sites on genomes according to the sequence pattern.},
}
@article {pmid33372473,
year = {2021},
author = {Zhang, HN and Cui, N and Shen, HM},
title = {[Metagenomic Analysis Provides Insights into Bacterial Communities, Antibiotic Resistomes, and Public Health Risks in the Dongping Lake Reservoir].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {42},
number = {1},
pages = {211-220},
doi = {10.13227/j.hjkx.202005305},
pmid = {33372473},
issn = {0250-3301},
abstract = {Owing to the long residence times of water, water reservoirs readily contribute to the accumulation of antibiotic resistant gene (ARG). It is of great public health significance to explore bacterial communities, antibiotic resistomes, and the potential public health risks of water reservoirs. In this study, metagenomic sequencing was used to analyze and compare the bacterial communities, ARG profiles, ARG-horizontal transfer, and ARG-carrying pathogens in the water and sediments of the Dongping Lake Reservoir in the dry and the wet seasons. Compared with that of the sediments, the results showed that both the bacterial communities and ARG profiles in the water were significantly influenced by the seasons, and the total ARG abundance in the dry season was significantly higher than that in the wet season. The total ARG abundance in the sediments was higher than that in water, but the horizontal transfer potential of ARG in the water was higher than that in the sediment. A total of 377 ARG subtypes belonging to 20 ARG types were found in this study. Bacitracin and vancomycin resistance genes were the main ARG types in the water and sediments, respectively, and Proteobacteria and Actinobacteria were the major ARG-carrying bacteria in the water and sediments, respectively. In addition, 30 clinical pathogens carrying ARGs were identified, including Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella enterica, and Acinetobacter bohemicus. More importantly, two Escherichia coli concurrently carried virulence factor and ARG. In summary, this study revealed that a variety of ARG types existed in the Dongping Lake Reservoir, which has posed potential public health risks by contributing to the horizontal transfer of ARG and the accumulation of clinical pathogens. Therefore, it is necessary to regularly monitor the bacterial community and ARG profile in various water bodies.},
}
@article {pmid33371686,
year = {2020},
author = {Jiang, L and Luo, C and Zhang, D and Song, M and Mei, W and Sun, Y and Zhang, G},
title = {Shifts in a Phenanthrene-Degrading Microbial Community are Driven by Carbohydrate Metabolism Selection in a Ryegrass Rhizosphere.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.0c04951},
pmid = {33371686},
issn = {1520-5851},
abstract = {Plants usually promote pollutant bioremediation by several mechanisms including modifying the diversity of functional microbial species. However, conflicting results are reported that root exudates have no effects or negative effects on organic pollutant degradation. In this study, we investigated the roles of ryegrass in phenanthrene degradation in soils using DNA stable isotope probing (SIP) and metagenomics to reveal a potential explanation for conflicting results among phytoremediation studies. Phenanthrene biodegradation efficiency was improved by 8% after 14 days of cultivation. Twelve and ten operational taxonomic units (OTUs) were identified as active phenanthrene degraders in non-rhizosphere and rhizosphere soils, respectively. The active phenanthrene degraders exhibited higher average phylogenetic distances in rhizosphere soils (0.33) than non-rhizosphere soils (0.26). The Ka/Ks values (the ratio of nonsynonymous to synonymous substitutions) were about 10.37% higher in the rhizosphere treatment among >90% of all key carbohydrate metabolism-related genes, implying that ryegrass may be an important driver of microbial community variation in the rhizosphere by relieving the carbohydrate metabolism pressure and improving the survival ability of r-strategy microbes. Most Ka/Ks values of root-exudate-related metabolism genes exhibited little change, except for fumarate hydratase that increased 13-fold in the rhizosphere compared to that in the non-rhizosphere treatment. The Ka/Ks values of less than 50% phenanthrene-degradation-related genes were affected, 30% of which increased and 70% behaved oppositely. Genes with altered Ka/Ks values had a low percentage and followed an inconsistent changing tendency, indicating that phenanthrene and its metabolites are not major factors influencing the active degraders. These results suggested the importance of carbohydrate metabolism, especially fumaric acid, in rhizosphere community shift, and hinted at a new hypothesis that the rhizosphere effect on phenanthrene degradation efficiency depends on the existence of active degraders that have competitive advantages in carbohydrate and fumaric acid metabolism.},
}
@article {pmid33364436,
year = {2019},
author = {Cresswell, FV and Davis, AG and Sharma, K and Basu Roy, R and Ganiem, AR and Kagimu, E and Solomons, R and Wilkinson, RJ and Bahr, NC and Thuong, NTT and , },
title = {Recent Developments in Tuberculous Meningitis Pathogenesis and Diagnostics.},
journal = {Wellcome open research},
volume = {4},
number = {},
pages = {164},
pmid = {33364436},
issn = {2398-502X},
abstract = {The pathogenesis of Tuberculous meningitis (TBM) is poorly understood, but contemporary molecular biology technologies have allowed for recent improvements in our understanding of TBM. For instance, neutrophils appear to play a significant role in the immunopathogenesis of TBM, and either a paucity or an excess of inflammation can be detrimental in TBM. Further, severity of HIV-associated immunosuppression is an important determinant of inflammatory response; patients with the advanced immunosuppression (CD4+ T-cell count of <150 cells/μL) having higher CSF neutrophils, greater CSF cytokine concentrations and higher mortality than those with CD4+ T-cell counts > 150 cells/μL. Host genetics may also influence outcomes with LT4AH genotype predicting inflammatory phenotype, steroid responsiveness and survival in Vietnamese adults with TBM. Whist in Indonesia, CSF tryptophan level was a predictor of survival, suggesting tryptophan metabolism may be important in TBM pathogenesis. These varying responses mean that we must consider whether a &quot;one-size-fits-all&quot; approach to anti-bacillary or immunomodulatory treatment in TBM is truly the best way forward. Of course, to allow for proper treatment, early and rapid diagnosis of TBM must occur. Diagnosis has always been a challenge but the field of TB diagnosis is evolving, with sensitivities of at least 70% now possible in less than two hours with GeneXpert MTB/Rif Ultra. In addition, advanced molecular techniques such as CRISPR-MTB and metagenomic next generation sequencing may hold promise for TBM diagnosis. Host-based biomarkers and signatures are being further evaluated in childhood and adult TBM as adjunctive biomarkers as even with improved molecular assays, cases are still missed. A better grasp of host and pathogen behaviour may lead to improved diagnostics, targeted immunotherapy, and possibly biomarker-based, patient-specific treatment regimens.},
}
@article {pmid33369664,
year = {2020},
author = {Díaz, L and Castellá, G and Bragulat, MR and Martorell, J and Paytuví-Gallart, A and Sanseverino, W and Cabañes, FJ},
title = {External ear canal mycobiome of some rabbit breeds.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myaa097},
pmid = {33369664},
issn = {1460-2709},
abstract = {The genus Malassezia is part of the normal skin mycobiota of a wide range of warm-blooded animals. In this genus, M. cuniculi is the only species described from rabbits. However, Malassezia species are rarely studied in lagomorphs. In the present study, the presence of Malassezia was assessed in samples from the external ear canal of healthy rabbits of different breeds. Cytological and culture techniques, Sanger sequencing, and Next-generation sequencing (NGS) were used to describe the ear mycobiota in the samples. Although no growth was observed in the cultured plates, cytological examination revealed the presence of round cells similar to those of Malassezia yeasts. For metagenomics analysis, the D1/D2 domain of the large subunit of the ribosomal DNA (LSU rDNA) was PCR amplified and the resulting reads were mapped against a custom-made cured database of 26S fungal sequences. NGS analysis revealed that Basidiomycota was the most abundant phylum in all the samples followed by Ascomycota. Malassezia was the most common genus presenting the highest abundance in the external ear canal. Malassezia phylotype 131 and M. cuniculi were the main sequences detected in the external auditory canal of rabbits. The study included both lop-eared and erect-eared rabbits and no differences were observed in the results when comparing both groups. This is the first attempt to study the external ear canal mycobiome of rabbits of different breeds using NGS.<br><br>LAY SUMMARY: In the present study, the presence of Malassezia was assessed in samples from the external ear canal of healthy rabbits of different breeds. Cytological and culture techniques, Sanger sequencing, and Next-generation sequencing (NGS) were used to describe the ear mycobiota in the samples.},
}
@article {pmid33369241,
year = {2020},
author = {Szoboszlay, M and Tebbe, CC},
title = {Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates.},
journal = {MicrobiologyOpen},
volume = {},
number = {},
pages = {e1144},
doi = {10.1002/mbo3.1144},
pmid = {33369241},
issn = {2045-8827},
support = {SPP2089//Helmholtz-Zentrum für Umweltforschung/ ; 403668538//German Research Foundation/ ; },
abstract = {Sequencing PCR-amplified gene fragments from metagenomic DNA is a widely applied method for studying the diversity and dynamics of soil microbial communities. Typically, DNA is extracted from 0.25 to 1 g of soil. These amounts, however, neglect the heterogeneity of soil present at the scale of soil aggregates and thus ignore a crucial scale for understanding the structure and functionality of soil microbial communities. Here, we show with a nitrogen-depleted agricultural soil the impact of reducing the amount of soil used for DNA extraction from 250 mg to approx. 1 mg to access spatial information on the prokaryotic community structure, as indicated by 16S rRNA gene amplicon analyses. Furthermore, we demonstrate that individual aggregates from the same soil differ in their prokaryotic community compositions. The analysis of 16S rRNA gene amplicon sequences from individual soil aggregates allowed us, in contrast to 250 mg soil samples, to construct a co-occurrence network that provides insight into the structure of microbial associations in the studied soil. Two dense clusters were apparent in the network, one dominated by Thaumarchaeota, known to be capable of ammonium oxidation at low N concentrations, and the other by Acidobacteria subgroup 6, representing an oligotrophic lifestyle to obtain energy from SOC. Overall this study demonstrates that DNA obtained from individual soil aggregates provides new insights into how microbial communities are assembled.},
}
@article {pmid33369229,
year = {2020},
author = {Fu, H and Zhang, L and Fan, C and Liu, C and Li, W and Cheng, Q and Zhao, X and Jia, S and Zhang, Y},
title = {Environment and host species identity shape gut microbiota diversity in sympatric herbivorous mammals.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.13687},
pmid = {33369229},
issn = {1751-7915},
support = {31670394//National Natural Science Foundation of China/ ; },
abstract = {The previous studies have reported that the mammalian gut microbiota is a physiological consequence; nonetheless, the factors influencing its composition and function remain unclear. In this study, to evaluate the contributions of the host and environment to the gut microbiota, we conducted a sequencing analysis of 16S rDNA and shotgun metagenomic DNA from plateau pikas and yaks, two sympatric herbivorous mammals, and further compared the sequences in summer and winter. The results revealed that both pikas and yaks harboured considerably more distinct communities between summer and winter. We detected the over-representation of Verrucomicrobia and Proteobacteria in pikas, and Archaea and Bacteroidetes in yaks. Firmicutes and Actinobacteria, associated with energy-efficient acquisition, significantly enriched in winter. The diversity of the microbial community was determined by the interactive effects between the host and season. Metagenomic analysis revealed that methane-metabolism-related pathway of yaks was significantly enriched in summer, while some pathogenic pathways were more abundant in pikas. Both pikas and yaks had a higher capacity for lipid degradation in winter. Pika and yak shared more OTUs when food shortage occurred in winter, and this caused a convergence in gut microbial composition and function. From winter to summer, the network module number increased from one to five in pikas, which was different in yaks. Our study demonstrates that the host is a dominant factor in shaping the microbial communities and that seasonality promotes divergence or convergence based on dietary quality across host species identity.},
}
@article {pmid33369160,
year = {2020},
author = {Waterworth, SC and Isemonger, EW and Rees, ER and Dorrington, RA and Kwan, JC},
title = {Conserved bacterial genomes from two geographically isolated peritidal stromatolite formations shed light on potential functional guilds.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12916},
pmid = {33369160},
issn = {1758-2229},
support = {6920//Gordon and Betty Moore Foundation/ ; DBI-1845890//National Science Foundation/ ; 109680//South African National Research Foundation/ ; 87583//South African National Research Foundation/ ; },
abstract = {Stromatolites are complex microbial mats that form lithified layers. Fossilized stromatolites are the oldest evidence of cellular life on Earth, dating back over 3.4 billion years. Modern stromatolites are relatively rare but may provide clues about the function and evolution of their ancient counterparts. In this study, we focus on peritidal stromatolites occurring at Cape Recife and Schoenmakerskop on the southeastern South African coastline, the former being morphologically and structurally similar to fossilized phosphatic stromatolites formations. Using assembled shotgun metagenomic analysis, we obtained 183 genomic bins, of which the most dominant taxa were from the Cyanobacteria phylum. We identified functional gene sets in genomic bins conserved across two geographically isolated stromatolite formations, which included relatively high copy numbers of genes involved in the reduction of nitrates and phosphatic compounds. Additionally, we found little evidence of Archaeal species in these stromatolites, suggesting that they may not play an important role in peritidal stromatolite formations, as proposed for hypersaline formations.},
}
@article {pmid33368907,
year = {2020},
author = {Garcia-Heredia, I and Bhattacharjee, AS and Fornas, O and Gomez, ML and Martínez, JM and Martinez-Garcia, M},
title = {Benchmarking of Single-Virus Genomics: a new tool for uncovering the virosphere.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15375},
pmid = {33368907},
issn = {1462-2920},
abstract = {Metagenomics and single-cell genomics have enabled the discovery of relevant uncultured microbes. Recently, single-virus genomics (SVG), although still in an incipient stage, has opened new avenues in viral ecology by allowing the sequencing of one single virus at a time. The investigation of methodological alternatives and optimization of existing procedures for SVG is paramount to deliver high-quality genomic data. We report a sequencing dataset of viral single-amplified genomes (vSAGs) from cultured and uncultured viruses obtained by applying different conditions in each SVG step, from viral preservation and novel whole-genome amplification (WGA) to sequencing platforms and genome assembly. Sequencing data showed that cryopreservation and mild fixation were compatible with WGA, although fresh samples delivered better genome quality data. The novel TruPrime WGA, based on primase-polymerase features, and WGA-X employing a thermostable phi29 polymerase, were proven to be with sufficient sensitivity in SVG. The Oxford Nanopore (ON) sequencing platform did not provide a significant improvement of vSAG assembly compared to Illumina alone. Finally, the SPAdes assembler performed the best. Overall, our results represent a valuable genomic dataset that will help to standardized and advance new tools in viral ecology. This article is protected by copyright. All rights reserved.},
}
@article {pmid33367889,
year = {2020},
author = {Okubo, T and Toyoda, A and Fukuhara, K and Uchiyama, I and Harigaya, Y and Kuroiwa, M and Suzuki, T and Murakami, Y and Suwa, Y and Takami, H},
title = {The physiological potential of anammox bacteria as revealed by their core genome structure.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaa028},
pmid = {33367889},
issn = {1756-1663},
abstract = {We present here the second complete genome of anaerobic ammonium oxidation (anammox) bacterium, Candidatus (Ca.) Brocadia pituitae, along with those of a nitrite oxidizer and two incomplete denitrifiers from the anammox bacterial community (ABC) metagenome. Although NO2- reduction to NO is considered to be the first step in anammox, Ca. B. pituitae lacks nitrite reductase genes (nirK and nirS) responsible for this reaction. Comparative genomics of Ca. B. pituitae with Ca. K. stuttgartiensis and six other anammox bacteria with nearly complete genomes revealed that their core genome structure contains 1,152 syntenic orthologs. But nitrite reductase genes were absent from the core, whereas two other Brocadia species possess nirK and these genes were horizontally acquired from multiple lineages. In contrast, at least 5 paralogous hydroxylamine oxidoreductase genes containing candidate ones (hao2 and hao3) encoding another nitrite reductase were observed in the core. Indeed, these two genes were also significantly expressed in Ca. B. pituitae as in other anammox bacteria. Because many nirS and nirK genes have been detected in the ABC metagenome, Ca. B. pituitae presumably utilises not only NO supplied by the ABC members but also NO and/or NH2OH by self-production for anammox metabolism.},
}
@article {pmid33367583,
year = {2020},
author = {Chen, H and Yin, Y and Gao, H and Guo, Y and Dong, Z and Wang, X and Zhang, Y and Yang, S and Peng, Q and Liu, Y and Wang, H},
title = {Clinical Utility of In-house Metagenomic Next-generation Sequencing for the Diagnosis of Lower Respiratory Tract Infections and Analysis of the Host Immune Response.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {71},
number = {Supplement_4},
pages = {S416-S426},
doi = {10.1093/cid/ciaa1516},
pmid = {33367583},
issn = {1537-6591},
abstract = {BACKGROUND: Only few pathogens that cause lower respiratory tract infections (LRTIs) can be identified due to limitations of traditional microbiological methods and the complexity of the oropharyngeal normal flora. Metagenomic next-generation sequencing (mNGS) has the potential to solve this problem.<br><br>METHODS: This prospective observational study sequentially enrolled 93 patients with LRTI and 69 patients without LRTI who visited Peking University People's Hospital in 2019. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS (DNA and RNA) and traditional microbiological assays. Human transcriptomes were compared between LRTI and non-LRTI, bacterial and viral LRTI, and tuberculosis and nontuberculosis groups.<br><br>RESULTS: Among 93 patients with LRTI, 20%, 35%, and 65% of cases were detected as definite or probable pathogens by culture, all microbiological tests, and mNGS, respectively. Our in-house BALF mNGS platform had an approximately 2-working-day turnaround time and detected more viruses and fungi than the other methods. Taking the composite reference standard as a gold standard, it had a sensitivity of 66.7%, specificity of 75.4%, positive-predictive value of 78.5%, and negative-predictive value of 62.7%. LRTI-, viral LRTI-, and tuberculosis-related differentially expressed genes were respectively related to immunity responses to infection, viral transcription and response to interferon-γ pathways, and perforin 1 and T-cell receptor B variable 9.<br><br>CONCLUSIONS: Metagenomic DNA and RNA-seq can identify a wide range of LRTI pathogens, with improved sensitivity for viruses and fungi. Our in-host platform is likely feasible in the clinic. Host transcriptome data are expected to be useful for the diagnosis of LRTIs.},
}
@article {pmid33365580,
year = {2019},
author = {Andújar, C and Arribas, P and Motyka, M and Bocek, M and Bocak, L and Linard, B and Vogler, AP},
title = {New mitochondrial genomes of 39 soil dwelling Coleoptera from metagenome sequencing.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {2447-2450},
pmid = {33365580},
issn = {2380-2359},
abstract = {High-throughput DNA methods hold great promise for the study of the hyperdiverse arthropod fauna of the soil. We used the mitochondrial metagenomic approach to generate 39 mitochondrial genomes from adult and larval specimens of Coleoptera collected from soil samples. The mitogenomes correspond to species from the families Carabidae (6), Chrysomelidae (1), Curculionidae (9), Dermestidae (1), Elateridae (1), Latridiidae (1), Scarabaeidae (3), Silvanidae (1), Staphylinidae (12), and Tenebrionidae (4). All the mitogenomes followed the putative ancestral gene order for Coleoptera. We provide the first available mitogenome for 30 genera of Coleoptera, including endogean representatives of the genera Torneuma, Coiffaitiella, Otiorhynchus, Oligotyphlopsis, and Typhlocharis.},
}
@article {pmid33365150,
year = {2020},
author = {Campbell, SJ and Ashley, W and Gil-Fernandez, M and Newsome, TM and Di Giallonardo, F and Ortiz-Baez, AS and Mahar, JE and Towerton, AL and Gillings, M and Holmes, EC and Carthey, AJR and Geoghegan, JL},
title = {Red fox viromes in urban and rural landscapes.},
journal = {Virus evolution},
volume = {6},
number = {2},
pages = {veaa065},
pmid = {33365150},
issn = {2057-1577},
abstract = {The Red fox (Vulpes vulpes) has established large populations in Australia's urban and rural areas since its introduction following European settlement. The cryptic and highly adaptable nature of foxes allows them to invade cities and live among humans whilst remaining largely unnoticed. Urban living and access to anthropogenic food resources also influence fox ecology. Urban foxes grow larger, live at higher densities, and are more social than their rural counterparts. These ecological changes in urban red foxes are likely to impact the pathogens that they harbour, and foxes could pose a disease risk to humans and other species that share these urban spaces. To investigate this possibility, we used a meta-transcriptomic approach to characterise the virome of urban and rural foxes across the Greater Sydney region in Australia. Urban and rural foxes differed significantly in virome composition, with rural foxes harbouring a greater abundance of viruses compared to their urban counterparts. We identified ten potentially novel vertebrate-associated viruses in both urban and rural foxes, some of which are related to viruses associated with disease in domestic species and humans. These included members of the Astroviridae, Picobirnaviridae, Hepeviridae, and Picornaviridae as well as rabbit haemorrhagic disease virus-2. This study sheds light on the viruses carried by urban and rural foxes and emphasises the need for greater genomic surveillance of foxes and other invasive species at the human-wildlife interface.},
}
@article {pmid33365020,
year = {2020},
author = {Santana-Pereira, ALR and Sandoval-Powers, M and Monsma, S and Zhou, J and Santos, SR and Mead, DA and Liles, MR},
title = {Discovery of Novel Biosynthetic Gene Cluster Diversity From a Soil Metagenomic Library.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {585398},
pmid = {33365020},
issn = {1664-302X},
abstract = {Soil microorganisms historically have been a rich resource for natural product discovery, yet the majority of these microbes remain uncultivated and their biosynthetic capacity is left underexplored. To identify the biosynthetic potential of soil microorganisms using a culture-independent approach, we constructed a large-insert metagenomic library in Escherichia coli from a topsoil sampled from the Cullars Rotation (Auburn, AL, United States), a long-term crop rotation experiment. Library clones were screened for biosynthetic gene clusters (BGCs) using either PCR or a NGS (next generation sequencing) multiplexed pooling strategy, coupled with bioinformatic analysis to identify contigs associated with each metagenomic clone. A total of 1,015 BGCs were detected from 19,200 clones, identifying 223 clones (1.2%) that carry a polyketide synthase (PKS) and/or a non-ribosomal peptide synthetase (NRPS) cluster, a dramatically improved hit rate compared to PCR screening that targeted type I polyketide ketosynthase (KS) domains. The NRPS and PKS clusters identified by NGS were distinct from known BGCs in the MIBiG database or those PKS clusters identified by PCR. Likewise, 16S rRNA gene sequences obtained by NGS of the library included many representatives that were not recovered by PCR, in concordance with the same bias observed in KS amplicon screening. This study provides novel resources for natural product discovery and circumvents amplification bias to allow annotation of a soil metagenomic library for a more complete picture of its functional and phylogenetic diversity.},
}
@article {pmid33364453,
year = {2020},
author = {Azad, MAK and Gao, J and Ma, J and Li, T and Tan, B and Huang, X and Yin, J},
title = {Opportunities of prebiotics for the intestinal health of monogastric animals.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {6},
number = {4},
pages = {379-388},
pmid = {33364453},
issn = {2405-6383},
abstract = {The goal of prebiotic applications from different sources is to improve the gut ecosystem where the host and microbiota can benefit from prebiotics. It has already been recognized that prebiotics have potential roles in the gut ecosystem because gut microbiota ferment complex dietary macronutrients and carry out a broad range of functions in the host body, such as the production of nutrients and vitamins, protection against pathogens, and maintenance of immune system balance. The gut ecosystem is very crucial and can be affected by numerous factors consisting of dietary constituents and commensal bacteria. This review focuses on recent scientific evidence, confirming a beneficial effect of prebiotics on animal health, particularly in terms of protection against pathogenic bacteria and increasing the number of beneficial bacteria that may improve epithelial cell barrier functions. It has also been reviewed that modification of the gut ecosystem through the utilization of prebiotics significantly affects the intestinal health of animals. However, the identification and characterization of novel potential prebiotics remain a topical issue and elucidation of the metagenomics relationship between gut microbiota alteration and prebiotic substances is necessary for future prebiotic studies.},
}
@article {pmid33363701,
year = {2020},
author = {Bokulich, NA and Ziemski, M and Robeson, MS and Kaehler, BD},
title = {Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {4048-4062},
pmid = {33363701},
issn = {2001-0370},
abstract = {Microbiomes are integral components of diverse ecosystems, and increasingly recognized for their roles in the health of humans, animals, plants, and other hosts. Given their complexity (both in composition and function), the effective study of microbiomes (microbiomics) relies on the development, optimization, and validation of computational methods for analyzing microbial datasets, such as from marker-gene (e.g., 16S rRNA gene) and metagenome data. This review describes best practices for benchmarking and implementing computational methods (and software) for studying microbiomes, with particular focus on unique characteristics of microbiomes and microbiomics data that should be taken into account when designing and testing microbiomics methods.},
}
@article {pmid33363050,
year = {2020},
author = {Kishikawa, T and Ogawa, K and Motooka, D and Hosokawa, A and Kinoshita, M and Suzuki, K and Yamamoto, K and Masuda, T and Matsumoto, Y and Nii, T and Maeda, Y and Nakamura, S and Inohara, H and Mochizuki, H and Okuno, T and Okada, Y},
title = {A Metagenome-Wide Association Study of Gut Microbiome in Patients With Multiple Sclerosis Revealed Novel Disease Pathology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {585973},
pmid = {33363050},
issn = {2235-2988},
abstract = {While microbiome plays key roles in the etiology of multiple sclerosis (MS), its mechanism remains elusive. Here, we conducted a comprehensive metagenome-wide association study (MWAS) of the relapsing-remitting MS gut microbiome (ncase = 26, ncontrol = 77) in the Japanese population, by using whole-genome shotgun sequencing. Our MWAS consisted of three major bioinformatic analytic pipelines (phylogenetic analysis, functional gene analysis, and pathway analysis). Phylogenetic case-control association tests showed discrepancies of eight clades, most of which were related to the immune system (false discovery rate [FDR] < 0.10; e.g., Erysipelatoclostridium_sp. and Gemella morbillorum). Gene association tests found an increased abundance of one putative dehydrogenase gene (Clo1100_2356) and one ABC transporter related gene (Mahau_1952) in the MS metagenome compared with controls (FDR < 0.1). Molecular pathway analysis of the microbiome gene case-control comparisons identified enrichment of multiple Gene Ontology terms, with the most significant enrichment on cell outer membrane (P = 1.5 × 10-7). Interaction between the metagenome and host genome was identified by comparing biological pathway enrichment between the MS MWAS and the MS genome-wide association study (GWAS) results (i.e., MWAS-GWAS interaction). No apparent discrepancies in alpha or beta diversities of metagenome were found between MS cases and controls. Our shotgun sequencing-based MWAS highlights novel characteristics of the MS gut microbiome and its interaction with host genome, which contributes to our understanding of the microbiome's role in MS pathophysiology.},
}
@article {pmid33363048,
year = {2020},
author = {Shi, W and Shen, L and Zou, W and Wang, J and Yang, J and Wang, Y and Liu, B and Xie, L and Zhu, J and Zhang, Z},
title = {The Gut Microbiome Is Associated With Therapeutic Responses and Toxicities of Neoadjuvant Chemoradiotherapy in Rectal Cancer Patients-A Pilot Study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {562463},
pmid = {33363048},
issn = {2235-2988},
abstract = {Responses to neoadjuvant chemoradiotherapy (nCRT) and therapy-related toxicities in rectal cancer vary among patients. To provide the individualized therapeutic option for each patient, predictive markers of therapeutic responses and toxicities are in critical need. We aimed to identify the association of gut microbiome with and its potential predictive value for therapeutic responses and toxicities. In the present study, we collected fecal microbiome samples from patients with rectal cancer at treatment initiation and just after nCRT. Taxonomic profiling via 16S ribosomal RNA gene sequencing was performed on all samples. Patients were classified as responders versus non-responders. Patients were grouped into no or mild diarrhea and severe diarrhea. STAMP and high-dimensional class comparisons via linear discriminant analysis of effect size (LEfSe) were used to compare the compositional differences between groups. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was utilized to predict differences in metabolic function between groups. Ten patients were classified as responders and 12 patients were classified as non-responders. Fourteen patients experienced no or mild diarrhea and 8 patients experienced severe diarrhea. Several bacteria taxa with significantly different relative abundances before and after nCRT were identified. Similarly, several baseline bacteria taxa and predicted pathways with significantly different relative abundances between responders and non-responders or between patients no or mild diarrhea and severe diarrhea were identified. Specifically, Shuttleworthia was identified as enriched in responders and several bacteria taxa in the Clostridiales order etc. were identified as enriched in non-responders. Pathways including fatty acid metabolism were predicted to be enriched in responders. In addition, Bifidobacterium, Clostridia, and Bacteroides etc. were identified as enriched in patients with no or mild diarrhea. Pathways including primary bile acid biosynthesis were predicted to be enriched in patients with no or mild diarrhea. Together, the microbiota and pathway markers identified in this study may be utilized to predict the therapeutic responses and therapy-related toxicities of nCRT in patients with rectal cancer. More patient data is needed to verify the current findings and the results of metagenomic, metatranscriptomic, and metabolomic analyses will further mine key biomarkers at the compositional and functional level.},
}
@article {pmid33362871,
year = {2020},
author = {Setubal, JC and Stoye, J and Dutilh, BE},
title = {Editorial: Computational Methods for Microbiome Analysis.},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {623897},
doi = {10.3389/fgene.2020.623897},
pmid = {33362871},
issn = {1664-8021},
}
@article {pmid33362241,
year = {2020},
author = {Laviad-Shitrit, S and Sela, R and Thorat, L and Sharaby, Y and Izhaki, I and Nath, BB and Halpern, M},
title = {Identification of chironomid species as natural reservoirs of toxigenic Vibrio cholerae strains with pandemic potential.},
journal = {PLoS neglected tropical diseases},
volume = {14},
number = {12},
pages = {e0008959},
doi = {10.1371/journal.pntd.0008959},
pmid = {33362241},
issn = {1935-2735},
abstract = {Vibrio cholerae causes the fatal cholera diarrhea. Chironomids (Diptera; Chironomidae) are abundant in freshwater aquatic habitats and estuaries and are natural reservoirs of V. cholerae. Until now, only the non-O1/O139 serogroups of V. cholerae were identified in chironomids. Here, we explored whether chironomids are natural reservoirs of V. cholerae O1/O139 serogroups, which are associated with cholera endemics and pandemics. All four life stages of chironomids were sampled from two rivers, and a laboratory culture in Pune, India, and from a pond in Israel. In total, we analyzed 223 chironomid samples. The presence of V. cholerae O1/O139 serogroups was verified using molecular tools. Nine chironomid species were identified; of them, Chironomus circumdatus was the most abundant. The presence of V. cholerae serogroup O1 and the cholera toxin genes were detected in samples from all chironomid species. However, serogroup O139 was detected in only two chironomid species. Besides PCR to detect specific genes, a metagenomic analysis that was performed in three selected C. ramosus larvae, identified a list of virulence genes associated with V. cholerae. The findings provide evidence that chironomids are natural reservoirs of toxigenic V. cholerae O1/O139. Chironomid populations and V. cholerae show biannual peak patterns. A similar pattern is found for cholera epidemics in the Bengal Delta region. Thus, we hypothesize that monitoring chironomids in endemic areas of the disease may provide a novel tool for predicting and preventing cholera epidemics. Moreover, serogroup O139 was detected only in two chironomid species that have a restricted distribution in the Indian subcontinent, possibly explaining why the distribution of the O139 serogroup is limited.},
}
@article {pmid33361322,
year = {2020},
author = {Dror, B and Wang, Z and Brady, SF and Jurkevitch, E and Cytryn, E},
title = {Elucidating the Diversity and Potential Function of Nonribosomal Peptide and Polyketide Biosynthetic Gene Clusters in the Root Microbiome.},
journal = {mSystems},
volume = {5},
number = {6},
pages = {},
pmid = {33361322},
issn = {2379-5077},
abstract = {Polyketides (PKs) and nonribosomal peptides (NRPs) are two microbial secondary metabolite (SM) families known for their variety of functions, including antimicrobials, siderophores, and others. Despite their involvement in bacterium-bacterium and bacterium-plant interactions, root-associated SMs are largely unexplored due to the limited cultivability of bacteria. Here, we analyzed the diversity and expression of SM-encoding biosynthetic gene clusters (BGCs) in root microbiomes by culture-independent amplicon sequencing, shotgun metagenomics, and metatranscriptomics. Roots (tomato and lettuce) harbored distinct compositions of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) relative to the adjacent bulk soil, and specific BGC markers were both enriched and highly expressed in the root microbiomes. While several of the highly abundant and expressed sequences were remotely associated with known BGCs, the low similarity to characterized genes suggests their potential novelty. Low-similarity genes were screened against a large set of soil-derived cosmid libraries, from which five whole BGCs of unknown function were retrieved. Three clusters were taxonomically affiliated with Actinobacteria, while the remaining were not associated with known bacteria. One Streptomyces-derived BGC was predicted to encode a polyene with potential antifungal activity, while the others were too novel to predict chemical structure. Screening against a suite of metagenomic data sets revealed higher abundances of retrieved clusters in roots and soil samples. In contrast, they were almost completely absent in aquatic and gut environments, supporting the notion that they might play an important role in root ecosystems. Overall, our results indicate that root microbiomes harbor a specific assemblage of undiscovered SMs.IMPORTANCE We identified distinct secondary-metabolite-encoding genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems yet almost completely absent in human gut and aquatic environments. Several of the genes were distantly related to genes encoding antimicrobials and siderophores, and their high sequence variability relative to known sequences suggests that they may encode novel metabolites and may have unique ecological functions. This study demonstrates that plant roots harbor a diverse array of unique secondary-metabolite-encoding genes that are highly enriched and expressed in the root ecosystem. The secondary metabolites encoded by these genes might assist the bacteria that produce them in colonization and persistence in the root environment. To explore this hypothesis, future investigations should assess their potential role in interbacterial and bacterium-plant interactions.},
}
@article {pmid33361321,
year = {2020},
author = {Sharma, AK and Petrzelkova, K and Pafco, B and Jost Robinson, CA and Fuh, T and Wilson, BA and Stumpf, RM and Torralba, MG and Blekhman, R and White, B and Nelson, KE and Leigh, SR and Gomez, A},
title = {Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions.},
journal = {mSystems},
volume = {5},
number = {6},
pages = {},
pmid = {33361321},
issn = {2379-5077},
abstract = {Compared with urban-industrial populations, small-scale human communities worldwide share a significant number of gut microbiome traits with nonhuman primates. This overlap is thought to be driven by analogous dietary triggers; however, the ecological and functional bases of this similarity are not fully understood. To start addressing this issue, fecal metagenomes of BaAka hunter-gatherers and traditional Bantu agriculturalists from the Central African Republic were profiled and compared with those of a sympatric western lowland gorilla group (Gorillagorilla gorilla) across two seasons of variable dietary intake. Results show that gorilla gut microbiomes shared similar functional traits with each human group, depending on seasonal dietary behavior. Specifically, parallel microbiome traits were observed between hunter-gatherers and gorillas when the latter consumed more structural polysaccharides during dry seasons, while small-scale agriculturalist and gorilla microbiomes showed significant functional overlap when gorillas consumed more seasonal ripe fruit during wet seasons. Notably, dominance of microbial transporters, transduction systems, and gut xenobiotic metabolism was observed in association with traditional agriculture and energy-dense diets in gorillas at the expense of a functional microbiome repertoire capable of metabolizing more complex polysaccharides. Differential abundance of bacterial taxa that typically distinguish traditional from industrialized human populations (e.g., Prevotella spp.) was also recapitulated in the human and gorilla groups studied, possibly reflecting the degree of polysaccharide complexity included in each group's dietary niche. These results show conserved functional gut microbiome adaptations to analogous diets in small-scale human populations and nonhuman primates, highlighting the role of plant dietary polysaccharides and diverse environmental exposures in this convergence.IMPORTANCE The results of this study highlight parallel gut microbiome traits in human and nonhuman primates, depending on subsistence strategy. Although these similarities have been reported before, the functional and ecological bases of this convergence are not fully understood. Here, we show that this parallelism is, in part, likely modulated by the complexity of plant carbohydrates consumed and by exposures to diverse xenobiotics of natural and artificial origin. Furthermore, we discuss how divergence from these parallel microbiome traits is typically associated with adverse health outcomes in human populations living under culturally westernized subsistence patterns. This is important information as we trace the specific dietary and environmental triggers associated with the loss and gain of microbial functions as humans adapt to various dietary niches.},
}
@article {pmid33361108,
year = {2020},
author = {Nilewski, S and Varatnitskaya, M and Masuch, T and Kusnezowa, A and Gellert, M and Baumann, AF and Lupilov, N and Kusnezow, W and Koch, MH and Eisenacher, M and Berkmen, M and Lillig, CH and Leichert, LI},
title = {Functional metagenomics of the Thioredoxin superfamily.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.RA120.016350},
pmid = {33361108},
issn = {1083-351X},
abstract = {Environmental sequence data of microbial communities now makes up the majority of public genomic information. The assignment of a function to sequences from these metagenomic sources is challenging, because organisms associated with the data are often uncharacterized and not cultivable. To overcome these challenges, we created a rationally designed expression library of metagenomic proteins covering the sequence space of the thioredoxin superfamily. This library of 100 individual proteins represents more than 22'000 thioredoxins found in the Global Ocean Sampling dataset. We screened this library for the functional rescue of Escherichia coli mutants lacking the thioredoxin-type reductase (∆trxA), isomerase (∆dsbC), or oxidase (∆dsbA). We were able to assign functions to more than a quarter of our representative proteins. The in vivo function of a given representative could not be predicted by phylogenetic relation but did correlate with the predicted isoelectric surface potential of the protein. Selected proteins were then purified and we determined their activity using a standard insulin reduction assay and measured their redox potential. An unexpected gel shift of protein E5 during the redox potential determination revealed a redox cycle distinct from that of typical thioredoxin-superfamily oxidoreductases. Instead of the intramolecular disulfide bond formation typical for thioredoxins, this protein forms an intermolecular disulfide between the attacking cysteines of two separate subunits during its catalytic cycle. Our functional metagenomic approach proved not only useful to assign in vivo functions to representatives of thousands of proteins, but also uncovered a novel reaction mechanism in a seemingly well-known protein superfamily.},
}
@article {pmid33360619,
year = {2020},
author = {Hu, L and Wang, H and Xu, P and Zhang, Y},
title = {Biomineralization of hypersaline produced water using microbially induced calcite precipitation.},
journal = {Water research},
volume = {190},
number = {},
pages = {116753},
doi = {10.1016/j.watres.2020.116753},
pmid = {33360619},
issn = {1879-2448},
abstract = {Reusing produced water (PW) as the subsequent hydraulic fracturing fluid is currently the most economical and dominant practice in the shale oil and gas industry. However, high Ca2+ present in PW needs to be removed prior to reuse to minimize the potential for well clogging and formation damage. In this study, the microbially induced calcite precipitation (MICP), as an emerging biomineralization technique mediated by ureolytic bacteria, was employed to remove Ca2+ and toxic contaminants from hypersaline PW for the first time. Batch and continuous studies demonstrated the feasibility of MICP for Ca2+ removal from hypersaline PW under low urea and nutrient conditions. Throughout the continuous biofiltration operation with biochar as the media, high removal efficiencies of Ca2+ (~96%), organic contaminants (~100%), and heavy metals (~100% for As, Cd, Mn and Ni, 92.2% for Ba, 94.2% for Sr) were achieved when PW co-treated with synthetic domestic wastewater (SDW) under the condition of PW:SDW = 1:1 &amp; urea 4 g/L. Metagenomic sequencing analysis showed that a stable ureolytic bacterial consortium (containing Sporosarcina and Arthrobacter at the genus level) was constructed in the continuous biofiltration system under hypersaline conditions, which may play a crucial role during the biomineralization process. Moreover, the combination of the MICP and ammonium recovery could significantly reduce the acute toxicity of PW towards Vibrio fischeri by 72%. This research provides a novel insight into the biomineralization of Ca2+ and heavy metals from hypersaline PW through the MICP technique. Considering the low cost and excellent treatment performance, the proposed process has the potential to be used for both hydraulic fracturing reuse and desalination pretreatment on a large scale.},
}
@article {pmid33360470,
year = {2020},
author = {Yang, Y and Fang, A and Feng, K and Liu, B and Xie, G and Li, H and Xing, D},
title = {Mini-metagenome analysis of psychrophilic electroactive biofilms based on single cell sorting.},
journal = {The Science of the total environment},
volume = {762},
number = {},
pages = {144328},
doi = {10.1016/j.scitotenv.2020.144328},
pmid = {33360470},
issn = {1879-1026},
abstract = {Understanding the metabolic function of psychrophilic electroactive bacteria is important for the investigation of extracellular electron transfer (EET) mechanisms under low temperatures (4-15 °C). In this study, Raman activated cell ejection coupled high throughput sequencing was used to accurately generate a mini-metagenome of psychrophilic bacterial community. Hierarchical cluster analysis of the Raman spectrum could accurately select the target Geobacter cluster. The high relative abundance of the membrane transport functional genes ftsEX in the biofilm community indicated an adaptation to reduced temperature, which aided survival of the electroactive bacteria under low temperature. The basal metabolism such as citrate cycle and glycolytic pathway maintained the electron pool for the EET process. The identification of iron (III) transport system genes in high abundance indicated their presence in an active metabolic reaction for potential electron transfer process. It showed the potential involvement c-type cytochromes (coxA and cox1) activity in EET. These results indicated that psychrophilic Geobacter had effective EET mediated by c-type cytochromes at low temperatures.},
}
@article {pmid33360357,
year = {2020},
author = {Zhao, J and Li, Y and Li, Y and Zhang, K and Zhang, H and Li, Y},
title = {Effects of humic acid on sludge performance, antibiotics resistance genes propagation and functional genes expression during Cu(II)-containing wastewater treatment via metagenomics analysis.},
journal = {Bioresource technology},
volume = {323},
number = {},
pages = {124575},
doi = {10.1016/j.biortech.2020.124575},
pmid = {33360357},
issn = {1873-2976},
abstract = {The humic acid (HA) function on the sludge performance, antibiotics resistance genes (ARGs) propagation and functional genes expression during Cu(II)-containing wastewater treatment was comprehensively investigated via metagenomics analysis. Results showed that the pollutants removal was significantly inhibited after long-term exposure of 5 mg/L Cu(II), while the inhibitory effects were moderately alleviated after addition of 10 mg/L HA. The extracellular polymeric substances (EPS) production with Cu(II) acclimation was higher than the sludge with Cu(II) and HA acclimation. The microbial community was significantly affected by the HA addition, while the relative abundance of dominant ARGs had no distinct differences with or without HA addition under Cu(II) stress. The functional genes were largely implemented for microbial metabolism, while no significant differences were found with HA addition under Cu(II) stress. Thus, the HA function for ARGs propagation and functional genes expression needed to be further research under Cu(II) stress in wastewater treatment.},
}
@article {pmid33360047,
year = {2020},
author = {Pastor-Villaescusa, B and Plaza-Díaz, J and Egea-Zorrilla, A and Leis, R and Bueno, G and Hoyos, R and Vázquez-Cobela, R and Latorre, M and Cañete, MD and Caballero-Villarraso, J and Gil, Á and Cañete, R and Aguilera, CM},
title = {Evaluation of the gut microbiota after metformin intervention in children with obesity: A metagenomic study of a randomized controlled trial.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {134},
number = {},
pages = {111117},
doi = {10.1016/j.biopha.2020.111117},
pmid = {33360047},
issn = {1950-6007},
abstract = {BACKGROUND: Metformin, a first-line oral antidiabetic agent that has shown promising results in terms of treating childhood and adolescent obesity, might influence the composition of the gut microbiota. We aimed to evaluate whether the gut microbiota of non-diabetic children with obesity changes after a metformin intervention.<br><br>METHODS: The study was a multicenter and double-blind randomized controlled trial in 160 children with obesity. Children were randomly assigned to receive either metformin (1 g/day) or placebo for 6 months in combination with healthy lifestyle recommendations in both groups. Then, we conducted a metagenomic analysis in a subsample obtained from 33 children (15 metformin, 18 placebo). A linear mixed-effects model (LMM) was used to determine the abundance changes from baseline to six months according to treatment. To analyze the data by clusters, a principal component analysis was performed to understand whether lifestyle habits have a different influence on the microbiota depending on the treatment group.<br><br>RESULTS: Actinobacteria abundance was higher after placebo treatment compared with metformin. However, the interaction time x treatment just showed a trend to be significant (4.6% to 8.1% after placebo vs. 3.8 % to 2.6 % after metformin treatment, p = 0.055). At genus level, only the abundance of Bacillus was significantly higher after the placebo intervention compared with metformin (2.5% to 5.7% after placebo vs. 1.5 % to 0.8 % after metformin treatment, p = 0.044). Furthermore, different ensembles formed by Firmicutes, Bacteroidetes, and Verrucomicrobia were found according to the interventions under a similar food consumption.<br><br>CONCLUSION: Further studies with a large sample size controlled by lifestyle patterns are required in obese children and adolescents to clarify whether metformin might trigger gut microbiota alterations.<br><br>TRIAL REGISTRATION: Registered on the European Clinical Trials Database (EudraCT, ID: 2010-023061-21) on 14 November 2011.},
}
@article {pmid33359946,
year = {2020},
author = {Liu, X and Chen, Y and Ouyang, H and Liu, J and Luo, X and Huang, Y and Chen, Y and Ma, J and Xia, J and Ding, L},
title = {Tuberculosis Diagnosis by Metagenomic Next-generation Sequencing on Bronchoalveolar Lavage Fluid: a cross-sectional analysis.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijid.2020.12.063},
pmid = {33359946},
issn = {1878-3511},
abstract = {BACKGROUND: Metagenomic Next-generation Sequencing (mNGS) has been shown as an effective diagnostic method for infectious diseases, but its potential clinical utility for tuberculosis (TB) diagnosis remains to be demonstrated.<br><br>METHODS: Three hundreds and twenty-two bronchoalveolar lavage fluid (BALF) samples collected from 311 suspected and confirmed pulmonary TB patients, were tested by mNGS, smear, Xpert® MTB/RIF (Xpert) and culture. The diagnostic performance of mNGS with conventional detection methods for Mycobacterium tuberculosis complex (MTBC) and other pathogens in BALF were compared. Additionally, the underlying factors associated with positive detection in pulmonary TB patients were investigated.<br><br>RESULTS: mNGS, Xpert and culture presented a high proportion of complete matching for MTBC detection (244/322, 75.8%). In the pulmonary TB patients before treatment, the sensitivity of MTBC detection by mNGS, Xpert, culture and smear was 59.9%(85/142), 69.0%(98/142), 59.9%(85/142) and 24.6%(35/142), respectively, and 79.6% overall, of which MTBC was detected by mNGS in 33.2% (5/34) Xpert and culture-negative samples. The positive MTBC detection by mNGS was affected by Vitamin D, ESR, TB initial treatment/retreatment and cavity in chest imaging (χ2 = 37.42, P < 0.001), but not by prior anti-TB usage within three months. mNGS was able to detect new potential pathogens in 8.7% (28/322) of samples.<br><br>CONCLUSIONS: Combined with mNGS based on conventional detection methods could increase the detection rate of MTBC. Additionally, mNGS could identify pathogens in a non-targeted approach for the better diagnosis of coinfection.},
}
@article {pmid33358876,
year = {2020},
author = {Du, J and Yin, Q and Gu, M and Wu, G},
title = {New insights into the effect of ethanol and volatile fatty acids proportions on methanogenic activities and pathways.},
journal = {Environmental research},
volume = {194},
number = {},
pages = {110644},
doi = {10.1016/j.envres.2020.110644},
pmid = {33358876},
issn = {1096-0953},
abstract = {During anaerobic digestion, methanogenic activities and pathways can be affected by intermediates. Here, the effects of intermediates acetate, propionate, and ethanol on methanogenesis were investigated. Four anaerobic sequencing batch reactors were acclimated with propionate (ASBR_P), ethanol/propionate (ASBR_EP), acetate/propionate (ASBR_AP), and ethanol/acetate/propionate (ASBR_EAP). Ethanol was the easiest one to be biodegraded, thereby enhancing the maximum methane production rate and shortening the lag phase, while the longest acclimation time and lowest methane production rate were observed in ASBR_P. Different microbial communities and syntrophic patterns existed in four reactors. Desulfovibrio and Geobacter were the dominant ethanol-oxidizing bacteria in ASBR_EP and ASBR_EAP, respectively. Both Desulfovibrio and Geobacter possessed the potential of extracellular electron transfer, which might be the advantage of ethanol dosage for enhancing methanogenesis through direct interspecies electron transfer. Methanosarcina was enriched in ASBR_P and ASBR_AP, while Methanosaeta in ASBR_EP and ASBR_EAP. Genes responsible for acetoclastic methanogenesis were significantly enriched in ASBR_EAP, possibly resulting in the highest methanogenic activity from acetate. Results from this study will advance the optimization of practical anaerobic systems, which can be achieved by regulating the intermediates with different fermenting pathways.},
}
@article {pmid33357110,
year = {2020},
author = {Kubacki, J and Fraefel, C and Bachofen, C},
title = {Implementation of next-generation sequencing for virus identification in veterinary diagnostic laboratories.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {},
number = {},
pages = {1040638720982630},
doi = {10.1177/1040638720982630},
pmid = {33357110},
issn = {1943-4936},
abstract = {The value of next-generation sequencing (NGS)-based applications for testing purposes in human medicine is widely recognized. Although NGS-based metagenomic screening may be of interest in veterinary medicine, in particular for intensively farmed livestock species such as pigs, there is a lack of protocols tailored to veterinary requirements, likely because of the high diversity of species and samples. Therefore, we developed an NGS-based protocol for use in veterinary virology and present here different applications in porcine medicine. To develop the protocol, each step of sample preparation was optimized using porcine samples spiked with various RNA and DNA viruses. The resulting protocol was tested with clinical samples previously confirmed to be positive for specific viruses by a diagnostic laboratory. Additionally, we validated the protocol in an NGS viral metagenomics ring trial and tested the protocol on viral multiplex reference material (NIBSC, U.K.). We applied our ViroScreen protocol successfully for 1) virus identification, 2) virus characterization, and 3) herd screening. We identified torque teno sus virus and atypical porcine pestivirus in a neurologic case, determined the full-length genome sequence of swine influenza A virus in field samples, and screened pigs using pen floor fecal samples and chewing rope liquid.},
}
@article {pmid33357075,
year = {2020},
author = {Young, KT and Lahmers, KK and Sellers, HS and Stallknecht, DE and Poulson, RL and Saliki, JT and Tompkins, SM and Padykula, I and Siepker, C and Howerth, EW and Todd, M and Stanton, JB},
title = {Randomly primed, strand-switching, MinION-based sequencing for the detection and characterization of cultured RNA viruses.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {},
number = {},
pages = {1040638720981019},
doi = {10.1177/1040638720981019},
pmid = {33357075},
issn = {1943-4936},
abstract = {RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false-negative detection results. Targeted detection methods have a limited ability to detect unknown viruses and often provide insufficient data to detect coinfections or identify antigenic variants. Random, deep sequencing is a method that can more fully detect and characterize RNA viruses and is often coupled with molecular techniques or culture methods for viral enrichment. We tested viral culture coupled with third-generation sequencing for the ability to detect and characterize RNA viruses. Cultures of bovine viral diarrhea virus, canine distemper virus (CDV), epizootic hemorrhagic disease virus, infectious bronchitis virus, 2 influenza A viruses, and porcine respiratory and reproductive syndrome virus were sequenced on the MinION platform using a random, reverse primer in a strand-switching reaction, coupled with PCR-based barcoding. Reads were taxonomically classified and used for reference-based sequence building using a stock personal computer. This method accurately detected and identified complete coding sequence genomes with a minimum of 20× coverage depth for all 7 viruses, including a sample containing 2 viruses. Each lineage-typing region had at least 26× coverage depth for all viruses. Furthermore, analyzing the CDV sample through a pipeline devoid of CDV reference sequences modeled the ability of this protocol to detect unknown viruses. Our results show the ability of this technique to detect and characterize dsRNA, negative- and positive-sense ssRNA, and nonsegmented and segmented RNA viruses.},
}
@article {pmid33356195,
year = {2020},
author = {Shi, LD and Xu, QJ and Liu, JY and Han, ZX and Zhu, YG and Zhao, HP},
title = {Will a Non-antibiotic Metalloid Enhance the Spread of Antibiotic Resistance Genes: The Selenate Story.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.0c05698},
pmid = {33356195},
issn = {1520-5851},
abstract = {The rapid emergence of antibiotic resistance genes (ARGs) has become an increasingly serious threat to public health. Previous studies illustrate the antibiotic-like effect of many substances. However, whether and how commonly used or existing non-antibiotic metalloids (e.g., selenate) would enhance ARG spread remains poorly known. Here, we tracked the long-term operation of a bioreactor continuously fed with selenate for more than 1000 days. Metagenomic sequencing identified 191 different ARGs, of which the total abundance increased significantly after the amendment of selenate. Network analyses showed that ARGs resisting multiple drugs had very similar co-occurrence patterns, implying a potentially larger health risk. Host classification not only indicated multidrug-resistant species but also distinguished the mechanism of ARG enrichment for vertical transfer and horizontal gene transfer. Genome reconstruction of an ARG host suggested that selenate and its bioreduction product selenite could stimulate the overproduction of intracellular reactive oxygen species, which was confirmed by the direct measurement. Bacterial membrane permeability, type IV pilus formation, and DNA repair and recombination were also enhanced, together facilitating the horizontal acquirement of ARGs. Overall, this study for the first time highlights the ARG emergence and dissemination induced by a non-antibiotic metalloid and identifies ARG as a factor to consider in selenate bioremediation.},
}
@article {pmid33356191,
year = {2020},
author = {Hu, C and Liu, M and Wan, T and Tang, L and Sun, B and Zhou, B and Lam, JCW and Lam, PKS and Chen, L},
title = {Disturbances in Microbial and Metabolic Communication across the Gut-Liver Axis Induced by a Dioxin-like Pollutant: An Integrated Metagenomics and Metabolomics Analysis.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.0c06884},
pmid = {33356191},
issn = {1520-5851},
abstract = {To determine how the aryl hydrocarbon receptor (AhR) signaling acts along the gut-liver axis, we employed an integrated metagenomic and metabolomic approach to comprehensively profile the microbial and metabolic networks. Adult zebrafish were exposed to a model agonist of the AhR: polychlorinated biphenyl (PCB) 126. The metagenomic analysis showed that PCB126 suppressed microbial activities related to primary bile acid metabolism in male intestines. Accordingly, a suite of primary bile acids consistently showed higher concentrations, suggesting that bacterial conversion of primary bile acids was blocked. PCB126 also disturbed bacterial metabolism of bile acids in female intestines, as revealed by higher concentrations of primary bile acids (e.g., chenodeoxycholic acid) and activation of the nuclear farnesoid X receptor signaling. In addition, PCB126 exposure impaired the metabolism of various essential vitamins (e.g., retinol, vitamin B6, and folate). Degradation of vitamin B6 by bacterial enzymes was inhibited in male intestines, resulting in its intestinal accumulation. However, PCB126 suppressed the bacterial metabolism of vitamins in female intestines, causing systematic deficiency of essential vitamins. Overall, we found that PCB126 exposure dysregulated gut microbial activities, consequently interrupting bile acid and vitamin metabolism along the gut-liver axis. The findings provided an insight of the AhR action in microbe-host metabolic communication related to PCBs.},
}
@article {pmid33354421,
year = {2020},
author = {Huyben, D and Rimoldi, S and Ceccotti, C and Montero, D and Betancor, M and Iannini, F and Terova, G},
title = {Effect of dietary oil from Camelina sativa on the growth performance, fillet fatty acid profile and gut microbiome of gilthead Sea bream (Sparus aurata).},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e10430},
pmid = {33354421},
issn = {2167-8359},
abstract = {Background: In the last two decades, research has focused on testing cheaper and sustainable alternatives to fish oil (FO), such as vegetable oils (VO), in aquafeeds. However, FO cannot be entirely replaced by VOs due to their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), particularly eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic (DHA; 22:6n-3) acids. The oilseed plant, Camelina sativa, may have a higher potential to replace FO since it can contains up to 40% of the omega-3 precursors α-linolenic acid (ALA; 18:3n-3) and linoleic acid (LA; 18:2n-6).<br><br>Methods: A 90-day feeding trial was conducted with 600 gilthead sea bream (Sparus aurata) of 32.92 ± 0.31 g mean initial weight fed three diets that replaced 20%, 40% and 60% of FO with CO and a control diet of FO. Fish were distributed into triplicate tanks per diet and with 50 fish each in a flow-through open marine system. Growth performance and fatty acid profiles of the fillet were analysed. The Illumina MiSeq platform for sequencing of 16S rRNA gene and Mothur pipeline were used to identify bacteria in the faeces, gut mucosa and diets in addition to metagenomic analysis by PICRUSt.<br><br>Results and Conclusions: The feed conversion rate and specific growth rate were not affected by diet, although final weight was significantly lower for fish fed the 60% CO diet. Reduced final weight was attributed to lower levels of EPA and DHA in the CO ingredient. The lipid profile of fillets were similar between the dietary groups in regards to total saturated, monounsaturated, PUFA (n-3 and n-6), and the ratio of n-3/n-6. Levels of EPA and DHA in the fillet reflected the progressive replacement of FO by CO in the diet and the EPA was significantly lower in fish fed the 60% CO diet, while ALA was increased. Alpha and beta-diversities of gut bacteria in both the faeces and mucosa were not affected by any dietary treatment, although a few indicator bacteria, such as Corynebacterium and Rhodospirillales, were associated with the 60% CO diet. However, lower abundance of lactic acid bacteria, specifically Lactobacillus, in the gut of fish fed the 60% CO diet may indicate a potential negative effect on gut microbiota. PICRUSt analysis revealed similar predictive functions of bacteria in the faeces and mucosa, although a higher abundance of Corynebacterium in the mucosa of fish fed 60% CO diet increased the KEGG pathway of fatty acid synthesis and may act to compensate for the lack of fatty acids in the diet. In summary, this study demonstrated that up to 40% of FO can be replaced with CO without negative effects on growth performance, fillet composition and gut microbiota of gilthead sea bream.},
}
@article {pmid33353182,
year = {2020},
author = {Mardanov, AV and Gruzdev, EV and Smolyakov, DD and Rudenko, TS and Beletsky, AV and Gureeva, MV and Markov, ND and Berestovskaya, YY and Pimenov, NV and Ravin, NV and Grabovich, MY},
title = {Genomic and Metabolic Insights into Two Novel Thiothrix Species from Enhanced Biological Phosphorus Removal Systems.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33353182},
issn = {2076-2607},
support = {20-14-00137//Russian Science Foundation/ ; 18-29-25016//Russian Foundation for Basic Research/ ; },
abstract = {Two metagenome-assembled genomes (MAGs), obtained from laboratory-scale enhanced biological phosphorus removal bioreactors, were analyzed. The values of 16S rRNA gene sequence identity, average nucleotide identity, and average amino acid identity indicated that these genomes, designated as RT and SSD2, represented two novel species within the genus Thiothrix, 'Candidatus Thiothrix moscowensis' and 'Candidatus Thiothrix singaporensis'. A complete set of genes for the tricarboxylic acid cycle and electron transport chain indicates a respiratory type of metabolism. A notable feature of RT and SSD2, as well as other Thiothrix species, is the presence of a flavin adenine dinucleotide (FAD)-dependent malate:quinone oxidoreductase instead of nicotinamide adenine dinucleotide (NAD)-dependent malate dehydrogenase. Both MAGs contained genes for CO2 assimilation through the Calvin-Benson-Bassam cycle; sulfide oxidation (sqr, fccAB), sulfur oxidation (rDsr complex), direct (soeABC) and indirect (aprBA, sat) sulfite oxidation, and the branched Sox pathway (SoxAXBYZ) of thiosulfate oxidation to sulfur and sulfate. All these features indicate a chemoorganoheterotrophic, chemolithoautotrophic, and chemolithoheterotrophic lifestyle. Both MAGs comprise genes for nitrate reductase and NO-reductase, while SSD2 also contains genes for nitrite reductase. The presence of polyphosphate kinase and exopolyphosphatase suggests that RT and SSD2 could accumulate and degrade polyhosphates during the oxic-anoxic growth cycle in the bioreactors, such as typical phosphate-accumulating microorganisms.},
}
@article {pmid33352712,
year = {2020},
author = {Selbmann, L and Benkő, Z and Coleine, C and de Hoog, S and Donati, C and Druzhinina, I and Emri, T and Ettinger, CL and Gladfelter, AS and Gorbushina, AA and Grigoriev, IV and Grube, M and Gunde-Cimerman, N and Karányi, ZÁ and Kocsis, B and Kubressoian, T and Miklós, I and Miskei, M and Muggia, L and Northen, T and Novak-Babič, M and Pennacchio, C and Pfliegler, WP and Pòcsi, I and Prigione, V and Riquelme, M and Segata, N and Schumacher, J and Shelest, E and Sterflinger, K and Tesei, D and U'Ren, JM and Varese, GC and Vázquez-Campos, X and Vicente, VA and Souza, EM and Zalar, P and Walker, AK and Stajich, JE},
title = {Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES.},
journal = {Life (Basel, Switzerland)},
volume = {10},
number = {12},
pages = {},
pmid = {33352712},
issn = {2075-1729},
abstract = {The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the &quot;Shed light in The daRk lineagES of the fungal tree of life&quot; (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments.},
}
@article {pmid33352125,
year = {2020},
author = {Gallot-Lavallée, L and Archibald, JM},
title = {Evolutionary Biology: Viral Rhodopsins Illuminate Algal Evolution.},
journal = {Current biology : CB},
volume = {30},
number = {24},
pages = {R1469-R1471},
doi = {10.1016/j.cub.2020.10.080},
pmid = {33352125},
issn = {1879-0445},
abstract = {A new metagenomics study has shown that marine viruses recently acquired genes encoding light-gated ion channels from green algae. These so-called channelrhodopsin genes may allow the viruses to manipulate the swimming behavior of the algae they infect.},
}
@article {pmid33351849,
year = {2020},
author = {Kempnich, MW and Sison-Mangus, MP},
title = {Presence and abundance of bacteria with the Type VI secretion system in a coastal environment and in the global oceans.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0244217},
doi = {10.1371/journal.pone.0244217},
pmid = {33351849},
issn = {1932-6203},
abstract = {Marine bacteria employ various strategies to maintain their competitive advantage over others in a mixed community. The use of Type VI Secretion Systems (T6SS), a protein secretion apparatus used as a molecular weapon for interbacterial competition and eukaryotic interactions, is one of the competitive strategies that is least studied among heterotrophic bacteria living in the water column. To get an insight into the temporal and spatial distribution of bacteria with T6SS in this portion of the marine environment, we examine the presence and abundance of T6SS-bearing bacteria at both local and global scales through the use of metagenome data from water samples obtained from the coast of Monterey Bay and the TARA Oceans project. We also track the abundance of T6SS-harboring bacteria through a two-year time series of weekly water samples in the same coastal site to examine the environmental factors that may drive their presence and abundance. Among the twenty-one T6SS-bearing bacterial genera examined, we found several genera assume a particle-attached lifestyle, with only a few genera having a free-living lifestyle. The abundance of T6SS-harboring bacteria in both niches negatively correlates with the abundance of autotrophs. Globally, we found that T6SS genes are much more abundant in areas with low biological productivity. Our data suggest that T6SS-harboring bacteria tend to be abundant spatially and temporally when organic resources are limited. This ecological study agrees with the patterns observed from several in vitro studies; that T6SS could be an adaptive strategy employed by heterotrophic bacteria to obtain nutrients or reduce competition when resources are in limited quantity.},
}
@article {pmid33351736,
year = {2020},
author = {Jahan, NA and Lindsey, LL and Larsen, PA},
title = {The Role of Peridomestic Rodents as Reservoirs for Zoonotic Foodborne Pathogens.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1089/vbz.2020.2640},
pmid = {33351736},
issn = {1557-7759},
abstract = {Although rodents are well-known reservoirs and vectors for a number of zoonoses, the functional role that peridomestic rodents serve in the amplification and transmission of foodborne pathogens is likely underappreciated. Clear links have been identified between commensal rodents and outbreaks of foodborne pathogens throughout Europe and Asia; however, comparatively little research has been devoted to studying this relationship in the United States. In particular, regional studies focused on specific rodent species and their foodborne pathogen reservoir status across the diverse agricultural landscapes of the United States are lacking. We posit that both native and invasive species of rodents associated with food-production pipelines are likely sources of seasonal outbreaks of foodborne pathogens throughout the United States. In this study, we review the evidence that identifies peridomestic rodents as reservoirs for foodborne pathogens, and we call for novel research focused on the metagenomic communities residing at the rodent-agriculture interface. Such data will likely result in the identification of new reservoirs for foodborne pathogens and species-specific demographic traits that might underlie seasonal enteric disease outbreaks. Moreover, we anticipate that a One Health metagenomic research approach will result in the discovery of new strains of zoonotic pathogens circulating in peridomestic rodents. Data resulting from such research efforts would directly inform and improve upon biosecurity efforts, ultimately serving to protect our food supply.},
}
@article {pmid33351707,
year = {2020},
author = {Chacon-Baca, E and Santos, A and Miguel Sarmiento, A and Luís, AT and Santisteban, M and Fortes, JC and Dávila, JM and Diaz-Curiel, JM and Grande, JA},
title = {Acid Mine Drainage as Energizing Microbial Niches for the Formation of Iron Stromatolites: The Tintillo River in Southwest Spain.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ast.2019.2164},
pmid = {33351707},
issn = {1557-8070},
abstract = {The Iberian Pyrite Belt in southwest Spain hosts some of the largest and diverse extreme acidic environments with textural variation across rapidly changing biogeochemical gradients at multiple scales. After almost three decades of studies, mostly focused on molecular evolution and metagenomics, there is an increasing awareness of the multidisciplinary potential of these types of settings, especially for astrobiology. Since modern automatized exploration on extraterrestrial surfaces is essentially based on the morphological recognition of biosignatures, a macroscopic characterization of such sedimentary extreme environments and how they look is crucial to identify life properties, but it is a perspective that most molecular approaches frequently miss. Although acid mine drainage (AMD) systems are toxic and contaminated, they offer at the same time the bioengineering tools for natural remediation strategies. This work presents a biosedimentological characterization of the clastic iron stromatolites in the Tintillo river. They occur as laminated terraced iron formations that are the most distinctive sedimentary facies at the Tintillo river, which is polluted by AMD. Iron stromatolites originate from fluvial abiotic factors that interact with biological zonation. The authigenic precipitation of schwertmannite and jarosite results from microbial-mineral interactions between mineral and organic matrices. The Tintillo iron stromatolites are composed of bacterial filaments and diatoms as Nitzschia aurariae, Pinnularia aljustrelica, Stauroneis kriegeri, and Fragilaria sp. Furthermore, the active biosorption and bioleaching of sulfur are suggested by the black and white coloration of microbial filaments inside stromatolites. AMD systems are hazardous due to physical, chemical, and biological agents, but they also provide biogeochemical sources with which to infer past geochemical conditions on Earth and inform exploration efforts on extraterrestrial surfaces in the future.},
}
@article {pmid33350920,
year = {2021},
author = {Anh, NT and Nhu, LNT and Hong, NTT and Phuc, TM and Tam, PTT and Huong, DT and Anh, TT and Deng, X and Nghia, HDT and Nguyen, TT and Van Hung, N and Thuan, ND and Phuong, PTH and Chau, NVV and Baker, S and Delwart, E and Thwaites, G and Van Tan, L and , },
title = {Viral Metagenomic Analysis of Cerebrospinal Fluid from Patients with Acute Central Nervous System Infections of Unknown Origin, Vietnam.},
journal = {Emerging infectious diseases},
volume = {27},
number = {1},
pages = {205-213},
pmid = {33350920},
issn = {1080-6059},
abstract = {Central nervous system (CNS) infection is a serious neurologic condition, although the etiology remains unknown in >50% of patients. We used metagenomic next-generation sequencing to detect viruses in 204 cerebrospinal fluid (CSF) samples from patients with acute CNS infection who were enrolled from Vietnam hospitals during 2012-2016. We detected 8 viral species in 107/204 (52.4%) of CSF samples. After virus-specific PCR confirmation, the detection rate was lowered to 30/204 (14.7%). Enteroviruses were the most common viruses detected (n = 23), followed by hepatitis B virus (3), HIV (2), molluscum contagiosum virus (1), and gemycircularvirus (1). Analysis of enterovirus sequences revealed the predominance of echovirus 30 (9). Phylogenetically, the echovirus 30 strains belonged to genogroup V and VIIb. Our results expanded knowledge about the clinical burden of enterovirus in Vietnam and underscore the challenges of identifying a plausible viral pathogen in CSF of patients with CNS infections.},
}
@article {pmid33350070,
year = {2020},
author = {Meziti, A and Nikouli, E and Hatt, JK and Konstantinidis, KT and Kormas, KA},
title = {Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15373},
pmid = {33350070},
issn = {1462-2920},
abstract = {Geothermal springs are essentially un-affected by environmental conditions aboveground as they are continuously supplied with subsurface water with little variability in chemistry. Therefore, changes in their microbial community composition and function, especially over a long period, are expected to be limited but this assumption has not yet been rigorously tested. Toward closing this knowledge gap, we applied whole metagenome sequencing to 17 water samples collected between 2010 and 2016 from the Thermopyles sulfur-rich geothermal springs in central Greece. As revealed by 16S rRNA gene fragments recovered in the metagenomes, Epsilonproteobacteria-related operational taxonomic units (OTUs) dominated most samples and grouping of samples based on OTU abundances exhibited no apparent seasonal pattern. Similarities between samples regarding functional gene content were high, with all samples sharing >70% similarity in functional pathways. These community-wide patterns were further confirmed by analysis of metagenome-assembled genomes (MAGs), which showed that novel species and genera of the chemoautotrophic Campylobacterales order dominated the springs. These MAGs carried different pathways for thiosulfate or sulfide oxidation coupled to carbon fixation pathways. Overall, our study showed that even in the long term, functions of microbial communities in a moderately hot terrestrial spring remain stable, presumably driving the corresponding stability in community structure. This article is protected by copyright. All rights reserved.},
}
@article {pmid33349699,
year = {2020},
author = {Nayfach, S and Camargo, AP and Schulz, F and Eloe-Fadrosh, E and Roux, S and Kyrpides, NC},
title = {CheckV assesses the quality and completeness of metagenome-assembled viral genomes.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {33349699},
issn = {1546-1696},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; 2016/23218-0//University of São Paulo | Pro-Reitoria de Pesquisa, Universidade de São Paulo (Dean's Office for Research,University of Sao Paulo)/ ; },
abstract = {Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.},
}
@article {pmid33349238,
year = {2020},
author = {Leung, CM and Li, D and Xin, Y and Law, WC and Zhang, Y and Ting, HF and Luo, R and Lam, TW},
title = {MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data.},
journal = {BMC genomics},
volume = {21},
number = {Suppl 6},
pages = {500},
pmid = {33349238},
issn = {1471-2164},
support = {ITS/331/17FP//Innovative and Technology Fund/ ; 27204518//General Research Fund/ ; 17208019//General Research Fund/ ; },
abstract = {BACKGROUND: Next-generation sequencing (NGS) enables unbiased detection of pathogens by mapping the sequencing reads of a patient sample to the known reference sequence of bacteria and viruses. However, for a new pathogen without a reference sequence of a close relative, or with a high load of mutations compared to its predecessors, read mapping fails due to a low similarity between the pathogen and reference sequence, which in turn leads to insensitive and inaccurate pathogen detection outcomes.<br><br>RESULTS: We developed MegaPath, which runs fast and provides high sensitivity in detecting new pathogens. In MegaPath, we have implemented and tested a combination of polishing techniques to remove non-informative human reads and spurious alignments. MegaPath applies a global optimization to the read alignments and reassigns the reads incorrectly aligned to multiple species to a unique species. The reassignment not only significantly increased the number of reads aligned to distant pathogens, but also significantly reduced incorrect alignments. MegaPath implements an enhanced maximum-exact-match prefix seeding strategy and a SIMD-accelerated Smith-Waterman algorithm to run fast.<br><br>CONCLUSIONS: In our benchmarks, MegaPath demonstrated superior sensitivity by detecting eight times more reads from a low-similarity pathogen than other tools. Meanwhile, MegaPath ran much faster than the other state-of-the-art alignment-based pathogen detection tools (and compariable with the less sensitivity profile-based pathogen detection tools). The running time of MegaPath is about 20 min on a typical 1 Gb dataset.},
}
@article {pmid33348904,
year = {2020},
author = {Muggia, L and Ametrano, CG and Sterflinger, K and Tesei, D},
title = {An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota.},
journal = {Life (Basel, Switzerland)},
volume = {10},
number = {12},
pages = {},
pmid = {33348904},
issn = {2075-1729},
abstract = {Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.},
}
@article {pmid33348551,
year = {2020},
author = {Kodio, A and Menu, E and Ranque, S},
title = {Eukaryotic and Prokaryotic Microbiota Interactions.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33348551},
issn = {2076-2607},
support = {Méditerranée Infection 10-IAHU-03//This work was supported by the French Government under the &quot;Investissements d'avenir&quot; (Investments for the Future) programme managed by the Agence Nationale de la Recherche (ANR, fr: National Agency for Research), (reference: Méditerranée Infection 10-IAH/ ; },
abstract = {The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host's immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g., antibiotic treatment), climate, season and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies were analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health.},
}
@article {pmid33348106,
year = {2020},
author = {Ren, X and Hao, S and Yang, C and Yuan, L and Zhou, X and Zhao, H and Yao, J},
title = {Alterations of intestinal microbiota in liver cirrhosis with muscle wasting.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {83},
number = {},
pages = {111081},
doi = {10.1016/j.nut.2020.111081},
pmid = {33348106},
issn = {1873-1244},
abstract = {OBJECTIVES: The intestinal microbiota plays an important role in the nutritional status and energy metabolism of the host. Liver cirrhosis is accompanied by muscle wasting or sarcopenia. The aim of this study was to to explore the changes in intestinal microbiota in patients with liver cirrhosis and muscle wasting by using metagenomics.<br><br>METHODS: This was a cross-sectional study of patients with (n = 30) and without (n = 30) muscle wasting and age- and sex-matched healthy controls (n = 30) to evaluate changes in intestinal microbiota by metagenomic gene sequencing. Muscle wasting was determined by the third lumbar vertebrae skeletal muscle index (L3 SMI).<br><br>RESULTS: The Shannon index, which represents species diversity, of patients in the muscle-wasting group (2.11 ± 0.88) was lower than in the non-muscle-wasting group (2.64 ± 0.68; P = 0.039), which was significantly lower than in the healthy control group (2.70 ± 0.53; P = 0.023). There were 17 microbial species with significant differences in relative abundance between the two groups (linear discriminant analysis score >2; P < 0.05). The relative abundance of Escherichia coli, Peptostreptococcus stomatis, and Bacteroides uniformis showed the most significant association with L3 SMI.<br><br>CONCLUSIONS: There were compositional alterations in intestinal microbiota in patients with liver cirrhosis and muscle wasting. L3 SMI is closely related to E. coli, P. stomatis, and B. uniformis in liver cirrhosis. Further interventional studies are needed to confirm whether improving intestinal microbiota can improve the nutritional status of patients with liver cirrhosis.},
}
@article {pmid33347881,
year = {2020},
author = {Iliev, ID and Cadwell, K},
title = {Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2020.06.100},
pmid = {33347881},
issn = {1528-0012},
abstract = {The intestinal microbiota comprises diverse fungal and viral components, in addition to bacteria. These microbes interact with the immune system and affect human physiology. Advances in metagenomics have associated inflammatory and autoimmune diseases with alterations in fungal and viral species in the gut. Studies of animal models have found that commensal fungi and viruses can activate host-protective immune pathways related to epithelial barrier integrity, but can also induce reactions that contribute to events associated with inflammatory bowel disease. Changes in our environment associated with modernization and the COVID-19 pandemic have exposed humans to new fungi and viruses, with unknown consequences. We review the lessons learned from studies of animal viruses and fungi commonly detected in the human gut and how these might affect health and intestinal disease.},
}
@article {pmid33347568,
year = {2020},
author = {Dehority, W and Janowski, AB and Messacar, K and Polgreen, PM and Beekmann, SE},
title = {Variability in the Use of Novel Diagnostic Technology in Children With Suspected Encephalitis and in the Management of Emerging Encephalitides by Pediatric Infectious Disease Providers.},
journal = {Journal of the Pediatric Infectious Diseases Society},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpids/piaa149},
pmid = {33347568},
issn = {2048-7207},
abstract = {We surveyed pediatric infectious disease physicians through the Infectious Disease Society of America's Emerging Infections Network regarding the diagnosis and management of encephalitis. We identified practice variations, particularly with the use of new diagnostic modalities and management of autoimmune encephalitides. These findings may inform the creation of updated management guidelines.},
}
@article {pmid33346799,
year = {2020},
author = {Wang, S and Jiang, Y and Li, S},
title = {PStrain: An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaa1056},
pmid = {33346799},
issn = {1367-4811},
abstract = {MOTIVATION: The microbial community plays an essential role in human diseases and physiological activities. The functions of microbes can differ due to strain-level differences in the genome sequences. Shotgun metagenomic sequencing allows us to profile the strains in microbial communities practically. However, current methods are underdeveloped due to the highly similar sequences among strains. We observe that strains genotypes at the same single nucleotide variant (SNV) locus can be speculated by the genotype frequencies. Also, the variants in different loci covered by the same reads can provide evidence that they reside on the same strain.<br><br>RESULTS: These insights inspire us to design PStrain, an optimization method that utilizes genotype frequencies and the reads which cover multiple SNV loci to profile strains iteratively based on SNVs in a set of MetaPhlAn2 marker genes. Compared to the state-of-art methods, PStrain, on average, improved the performance of inferring strains abundances and genotypes by 87.75% and 59.45%, respectively. We have applied the PStrain package to the dataset with two cohorts of colorectal cancer (CRC) and found that the sequences of Bacteroides coprocola strains are significantly different between CRC and control samples, which is the first time to report the potential role of B. coprocola in the gut microbiota of CRC.<br><br>AVAILABILITY: https://github.com/wshuai294/PStrain.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid33346086,
year = {2020},
author = {Kang, J and Ciampi, A and Hijri, M},
title = {SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.gpb.2018.07.010},
pmid = {33346086},
issn = {2210-3244},
abstract = {Arbuscular mycorrhizal fungi (AMF) are plant root symbionts that play key roles in plant growth and soil fertility. They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores. Numerous studies have shown that diverse microorganisms live on the surface of and inside their mycelia, resulting in a metagenome when whole-genome sequencing (WGS) data are obtained from sequencing AMF cultivated in vivo. The metagenome contains not only the AMF sequences, but also those from associated microorganisms. In this article, we introduce a novel bioinformatics program, Spore associated Symbiotic Microbes (SeSaMe), designed for taxonomic classification of short sequences obtained by next-generation DNA sequencing. A genus-specific usage bias database was created based on amino acid usage and codon usage of three consecutive codon DNA 9-mer encoding an amino acid trimer in a protein secondary structure. The program distinguishes between coding sequence (CDS) and non-CDS, and classifies a query sequence into a genus group out of 54 genera used as reference. The mean percentages of correct predictions of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria, 65% and 73% for fungi (excluding AMF), and 49% and 72% for AMF (Rhizophagus irregularis), respectively. SeSaMe provides a means for estimating not only taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF. Therefore, it enables users to study the symbiotic roles of associated microorganisms. It can also be applicable to other microorganisms as well as soil metagenomes. SeSaMe is freely available at www.fungalsesame.org.},
}
@article {pmid33346085,
year = {2020},
author = {Eun Kang, J and Ciampi, A and Hijri, M},
title = {SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.gpb.2018.07.011},
pmid = {33346085},
issn = {2210-3244},
abstract = {In this article, we introduce a novel bioinformatics program, Spore-associated Symbiotic Microbes Position-Specific Function (SeSaMe PS Function), for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi. The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure, namely amino acid usages, codon usages, and codon contexts of 3-codon DNA 9-mers. SeSaMe PS Function searches a query sequence against reference sequence database, identifies 3-codon DNA 9-mers with structural roles, and creates comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera. The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset. 3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions. The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications. SeSaMe PS Function is available for free downloading at www.fungalsesame.org.},
}
@article {pmid33344092,
year = {2020},
author = {Vaz, ABM and Fonseca, PLC and Silva, FF and Quintanilha-Peixoto, G and Sampedro, I and Siles, JA and Carmo, A and Kato, RB and Azevedo, V and Badotti, F and Ocampo, JA and Rosa, CA and Góes-Neto, A},
title = {Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e10487},
pmid = {33344092},
issn = {2167-8359},
abstract = {The true myrtle, Myrtus communis, is a small perennial evergreen tree that occurs in Europe, Africa, and Asia with a circum-Mediterranean geographic distribution. Unfortunately, the Mediterranean Forests, where M. communis occurs, are critically endangered and are currently restricted to small fragmented areas in protected conservation units. In the present work, we performed, for the first time, a metabarcoding study on the spatial variation of fungal community structure in the foliar endophytome of this endemic plant of the Mediterranean biome, using bipartite network analysis as a model. The local bipartite network of Myrtus communis individuals and their foliar endophytic fungi is very low connected, with low nestedness, and moderately high specialization and modularity. Similar network patterns were also retrieved in both culture-dependent and amplicon metagenomics of foliar endophytes in distinct arboreal hosts in varied biomes. Furthermore, the majority of putative fungal endophytes species were basidiomycete woody saprotrophs of the orders Polyporales, Agaricales, and Hymenochaetales. Altogether, these findings suggest a possible adaptation of these wood-decaying fungi to cope with moisture limitation and spatial scarcity of their primary substrate (dead wood), which are totally consistent with the predictions of the viaphytism hypothesis that wood-decomposing fungi inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia, during periods of environmental stress.},
}
@article {pmid33343536,
year = {2020},
author = {Yin, X and Altman, T and Rutherford, E and West, KA and Wu, Y and Choi, J and Beck, PL and Kaplan, GG and Dabbagh, K and DeSantis, TZ and Iwai, S},
title = {A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {595910},
pmid = {33343536},
issn = {1664-302X},
support = {R44 DA043954/DA/NIDA NIH HHS/United States ; },
abstract = {Metabolomic analyses of human gut microbiome samples can unveil the metabolic potential of host tissues and the numerous microorganisms they support, concurrently. As such, metabolomic information bears immense potential to improve disease diagnosis and therapeutic drug discovery. Unfortunately, as cohort sizes increase, comprehensive metabolomic profiling becomes costly and logistically difficult to perform at a large scale. To address these difficulties, we tested the feasibility of predicting the metabolites of a microbial community based solely on microbiome sequencing data. Paired microbiome sequencing (16S rRNA gene amplicons, shotgun metagenomics, and metatranscriptomics) and metabolome (mass spectrometry and nuclear magnetic resonance spectroscopy) datasets were collected from six independent studies spanning multiple diseases. We used these datasets to evaluate two reference-based gene-to-metabolite prediction pipelines and a machine-learning (ML) based metabolic profile prediction approach. With the pre-trained model on over 900 microbiome-metabolome paired samples, the ML approach yielded the most accurate predictions (i.e., highest F1 scores) of metabolite occurrences in the human gut and outperformed reference-based pipelines in predicting differential metabolites between case and control subjects. Our findings demonstrate the possibility of predicting metabolites from microbiome sequencing data, while highlighting certain limitations in detecting differential metabolites, and provide a framework to evaluate metabolite prediction pipelines, which will ultimately facilitate future investigations on microbial metabolites and human health.},
}
@article {pmid33342997,
year = {2020},
author = {Viver, T and Conrad, RE and Orellana, LH and Urdiain, M and González-Pastor, JE and Hatt, JK and Amann, R and Antón, J and Konstantinidis, KT and Rosselló-Móra, R},
title = {Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {33342997},
issn = {1751-7370},
support = {PGC2018-096956-B-C41//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; PGC2018-096956-B-C41//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; },
abstract = {Microbial communities thriving in hypersaline brines of solar salterns are highly resistant and resilient to environmental changes, and salinity is a major factor that deterministically influences community structure. Here, we demonstrate that this resilience occurs even after rapid osmotic shocks caused by a threefold change in salinity (a reduction from 34 to 12% salts) leading to massive amounts of archaeal cell lysis. Specifically, our temporal metagenomic datasets identified two co-occurring ecotypes within the most dominant archaeal population of the brines Haloquadratum walsbyi that exhibited different salt concentration preferences. The dominant ecotype was generally more abundant and occurred in high-salt conditions (34%); the low abundance ecotype always co-occurred but was enriched at salinities around 20% or lower and carried unique gene content related to solute transport and gene regulation. Despite their apparent distinct ecological preferences, the ecotypes did not outcompete each other presumably due to weak functional differentiation between them. Further, the osmotic shock selected for a temporal increase in taxonomic and functional diversity at both the Hqr. walsbyi population and whole-community levels supporting the specialization-disturbance hypothesis, that is, the expectation that disturbance favors generalists. Altogether, our results provide new insights into how intraspecies diversity is maintained in light of substantial gene-content differences and major environmental perturbations.},
}
@article {pmid33342083,
year = {2020},
author = {Höppner, A and Bollinger, A and Kobus, S and Thies, S and Coscolín, C and Ferrer, M and Jaeger, KE and Smits, SHJ},
title = {Crystal structures of a novel family IV esterase in free and substrate-bound form.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.15680},
pmid = {33342083},
issn = {1742-4658},
abstract = {Bacterial lipolytic enzymes of family IV are homologs of the mammalian hormone-sensitive lipases (HSL) and have been successfully used for various biotechnological applications. The broad substrate specificity and ability for enantio-, regio-, and stereoselective hydrolysis are remarkable features of enzymes from this class. Many crystal structures are available for esterases and lipases, but structures of enzyme-substrate or enzyme-inhibitor complexes are less frequent although important to understand the molecular basis of enzyme substrate interaction and to rationalize biochemical enzyme characteristics. Here, we report on the structures of a novel family IV esterase isolated from a metagenomic screen which shows a broad substrate specificity. We solved the crystal structures in the apo form and with a bound substrate analogue at 1.35 Å and 1.81 Å resolution, respectively. This enzyme named PtEst1 hydrolyzed more than 60 out 96 structurally different ester substrates thus being substrate promiscuous. Its broad substrate specificity is in accord with a large active site cavity, which is covered by an α-helical cap domain. The substrate analogue methyl 4-methylumbelliferyl hexylphosphonate was rapidly hydrolyzed by the enzyme leading to a complete inactivation caused by covalent binding of phosphinic acid to the catalytic serine. Interestingly, the alcohol leaving group 4-methylumbelliferone was found remaining in the active site cavity and additionally, a complete inhibitor molecule was found at the cap domain next to the entrance of the substrate tunnel. This unique situation allowed gaining valuable insights into the role of the cap domain for enzyme-substrate interaction of esterases belonging to family IV.},
}
@article {pmid33341726,
year = {2020},
author = {Martínez-Gallardo, MR and López, MJ and López-González, JA and Jurado, MM and Suárez-Estrella, F and Pérez-Murcia, MD and Sáez, JA and Moral, R and Moreno, J},
title = {Microbial communities of the olive mill wastewater sludge stored in evaporation ponds: The resource for sustainable bioremediation.},
journal = {Journal of environmental management},
volume = {279},
number = {},
pages = {111810},
doi = {10.1016/j.jenvman.2020.111810},
pmid = {33341726},
issn = {1095-8630},
abstract = {Olive Mill Wastewater (OMW) is a polluting residue from the olive oil industry. It is usually stored in open-air unprotected evaporation ponds where their sediments accumulate. This study compares the characteristics of OMW sludges stored for long-time in evaporation ponds and assesses their impact on the underlying soil layer. Physicochemical parameters, toxicity bioassays, and full characterization of the microbial community were analyzed. The extension of the polluting effects was assessed by analysis of toxicity, microbial biomass carbon, and respiration. Geostatistics was used to predict their spatial distribution. Organic matter and polyphenol content besides toxicity levels determine variations between OMW sludges and have a high impact on the microbiota they contain. The microbial community was abundant, diverse, and functionally active. However, the biodegradability of the sludges was hindered by the toxicity levels. Toxicity and biomass carbon were higher on the surface of the ponds than in the soil layer revealing a reduced leach flow and depletion of contaminants. The natural microbiota might be biostimulated by means of applying sustainable and feasible biological treatments in order to favor the OMW sludges bioremediation. These results open up the possibility of solving the environmental concern caused by its storage in similar scenarios, which are common in olive oil-producing countries.},
}
@article {pmid33339953,
year = {2020},
author = {Kwun, JS and Kang, SH and Lee, HJ and Park, HK and Lee, WJ and Yoon, CH and Suh, JW and Cho, YS and Youn, TJ and Chae, IH},
title = {Comparison of thrombus, gut, and oral microbiomes in Korean patients with ST-elevation myocardial infarction: a case-control study.},
journal = {Experimental &amp; molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {33339953},
issn = {2092-6413},
support = {2019R1C1C1006611//National Research Foundation of Korea (NRF)/ ; },
abstract = {ST-segment elevation myocardial infarction (STEMI) is characterized by thrombotic coronary artery occlusions caused by atherosclerotic plaque rupture. The gut microbiome potentially contributes to the pathogenesis of coronary artery diseases. This study investigated the microbial diversity and composition of coronary thrombi in STEMI patients and the composition of the thrombus microbiome relative to that of the oral and gut microbiomes. A case-control study was performed with 22 STEMI patients and 20 age- and sex-matched healthy controls. Coronary thrombi were acquired from STEMI patients via manual thrombus aspiration during primary coronary intervention. Oral swab and stool samples were collected from both groups, and 16S rRNA sequencing and metagenomic microbiome analyses were performed. Microbial DNA was detected in 4 of 22 coronary thrombi. Proteobacteria (p) and Bacteroidetes (p) were the most abundant phyla. The oral and gut microbiomes significantly differed between patients and healthy controls. The patient group presented microbial dysbiosis, as follows: a higher relative abundance of Proteobacteria (p) and Enterobacteriaceae (f) in the gut microbiome and a lower abundance of Firmicutes (p) and Haemophilus (g) in the oral microbiome. Furthermore, 4 significantly abundant genera were observed in the coronary thrombus in the patients: Escherichia, 1.25%; Parabacteroides, 0.25%; Christensenella, 0.0%; and Bacteroides, 7.48%. The present results indicate that the relative abundance of the gut and oral microbiomes was correlated with that of the thrombus microbiome.},
}
@article {pmid33339826,
year = {2019},
author = {Pareek, S and Kurakawa, T and Das, B and Motooka, D and Nakaya, S and Rongsen-Chandola, T and Goyal, N and Kayama, H and Dodd, D and Okumura, R and Maeda, Y and Fujimoto, K and Nii, T and Ogawa, T and Iida, T and Bhandari, N and Kida, T and Nakamura, S and Nair, GB and Takeda, K},
title = {Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi.},
journal = {NPJ biofilms and microbiomes},
volume = {5},
number = {1},
pages = {37},
pmid = {33339826},
issn = {2055-5008},
support = {JP15H02511//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; JP15J06509//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation of adaptive immunity. In addition, commensal fungi residing in the intestine also influence host health. Although the interaction of bacterium and fungus has been shown, its precise mechanism during colonization of the human intestine remains largely unknown. Here, we show interaction between bacterial and fungal species for utilization of dietary components driving their efficient growth in the intestine. Next generation sequencing of fecal samples from Japanese and Indian adults revealed differential patterns of bacterial and fungal composition. In particular, Indians, who consume more plant polysaccharides than Japanese, harbored increased numbers of Prevotella and Candida. Candida spp. showed strong growth responses to the plant polysaccharide arabinoxylan in vitro. Furthermore, the culture supernatants of Candida spp. grown with arabinoxylan promoted rapid proliferation of Prevotella copri. Arabinose was identified as a potential growth-inducing factor in the Candida culture supernatants. Candida spp. exhibited a growth response to xylose, but not to arabinose, whereas P. copri proliferated in response to both xylose and arabinose. Candida spp., but not P. copri, colonized the intestine of germ-free mice. However, P. copri successfully colonized mouse intestine already harboring Candida. These findings demonstrate a proof of concept that fungal members of gut microbiota can facilitate a colonization of the intestine by their bacterial counterparts, potentially mediated by a dietary metabolite.},
}
@article {pmid33339094,
year = {2020},
author = {Bandarupalli, VVK and St-Pierre, B},
title = {Identification of a Candidate Starch Utilizing Strain of Prevotella albensis from Bovine Rumen.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33339094},
issn = {2076-2607},
support = {SD00H551-15//USDA National Institute of Food and Agriculture (Hatch)/ ; SD00H392-11//South Dakota State University Agricultural Experiment Station/ ; },
abstract = {The inclusion of starch-rich feedstuffs, a common practice in intensive ruminant livestock production systems, can result in ruminal acidosis, a condition that can severely impact animal performance and health. One of the main causes of acidosis is the rapid accumulation of ruminal short chain fatty acids (SCFAs) resulting from the microbial digestion of starch. A greater understanding of ruminal bacterial amylolytic activities is therefore critical to improving mitigation of acidosis. To this end, our manuscript reports the identification of a candidate starch utilizer (OTU SD_Bt-00010) using batch culturing of bovine rumen fluid supplemented with starch. Based on 16S rRNA gene sequencing and metagenomics analysis, SD_Bt-00010 is predicted to be a currently uncharacterized strain of Prevotella albensis. Annotation of de novo assembled contigs from metagenomic data not only identified sequences encoding for α-amylase enzymes, but also revealed the potential to metabolize xylan as an alternative substrate. Metagenomics also predicted that SCFA end products for SD_Bt-00010 would be acetate and formate, and further suggested that this candidate strain may be a lactate utilizer. Together, these results indicate that SD_Bt-00010 is an amylolytic symbiont with beneficial attributes for its ruminant host.},
}
@article {pmid33338948,
year = {2021},
author = {Hause, BM and Pillatzki, A and Clement, T and Bragg, T and Ridpath, J and Chase, CCL},
title = {Persistent infection of American bison (Bison bison) with bovine viral diarrhea virus and bosavirus.},
journal = {Veterinary microbiology},
volume = {252},
number = {},
pages = {108949},
doi = {10.1016/j.vetmic.2020.108949},
pmid = {33338948},
issn = {1873-2542},
abstract = {Bovine viral diarrhea viruses (BVDV) are significant pathogens of cattle, leading to losses associated with reproductive failure, respiratory disease and immune dysregulation. While cattle are the reservoir for BVDV, a wide range of domestic and wild ruminants are susceptible to infection and disease caused by BVDV. Samples from four American bison (Bison bison) from a captive herd were submitted for diagnostic testing due to their general unthriftiness. Metagenomic sequencing on pooled nasal swabs and serum identified co-infection with a BVDV and a bovine bosavirus. The BVDV genome was more similar to the vaccine strain Oregon C24 V than to other BVDV sequences in GenBank, with 92.7 % nucleotide identity in the open reading frame. The conserved 5'-untranslated region was 96.3 % identical to Oregon C24 V. Bosavirus has been previously identified in pooled fetal bovine serum but its clinical significance is unknown. Sequencing results were confirmed by virus isolation and PCR detection of both viruses in serum and nasal swab samples from two of the four bison. One animal was co-infected with both BVDV and bosavirus while separate individuals were positive solely for BVDV or bosavirus. Serum and nasal swabs from these same animals collected 51 days later remained positive for BVDV and bosavirus. These results suggest that both viruses can persistently infect bison. While the etiological significance of bosavirus infection is unknown, the ability of BVDV to persistently infect bison has implications for BVDV control and eradication programs. Possible synergy between BVDV and bosavirus persistent infection warrants further study.},
}
@article {pmid33338689,
year = {2020},
author = {Abou-Kandil, A and Shibli, A and Azaizeh, H and Wolff, D and Wick, A and Jadoun, J},
title = {Fate and removal of bacteria and antibiotic resistance genes in horizontal subsurface constructed wetlands: Effect of mixed vegetation and substrate type.},
journal = {The Science of the total environment},
volume = {759},
number = {},
pages = {144193},
doi = {10.1016/j.scitotenv.2020.144193},
pmid = {33338689},
issn = {1879-1026},
abstract = {This study aimed to investigate the influence of cropping method and substrate type on the fate and the removal of bacterial and antibiotic resistance genes (ARGs) indicators from primary wastewater by constructed wetlands (CWs) during startup and maturation stages. Four small-scale CWs differing in their plantation pattern (monoculture vs. polyculture) and substrate type were constructed and operated under field conditions. While for bacteria, the greatest impact of the cropping method and substrate type on removal was during the startup stage rather than the maturation stage, for ARGs, such impact was significant at both stages. During startup, the removal efficiencies of heterotrophic bacteria, fecal coliforms, E. coli, 16S rRNA genes and lacZ increased with the operation time. At maturation, the removal efficiencies were constant and were within the range of 89.2-99.4%, 93.7-98.9%, 89-98.8%, 94.1-99.6% and 92.9-98.7%, respectively. The removal efficiencies of intl1, tetM, intl1, sul1, ermB and total ARGs were also increased with the operation time. However, they were ARG type and configuration-dependent; at maturation they ranged between 50.7%-89.4%, 85.9%-97%, 49.6%-92.9%, 58.2%-96.7% and 79.9-94.3%, respectively. The tuff-filled serially planted CW was also the only one capable of removing these genes at similar high efficiency. Metagenomic analysis showed that none of the ARGs was among the most common ARGs in water and biofilm samples; rather most ARGs belonged to bacterial efflux transporter superfamilies. Although ARGs were removed, they were still detected in substrate biofilm and their relative concentrations were increased in the effluents. While the removal of both bacteria and ARGs was higher during summer compared to winter, the season had no effect on the removal pattern of ARGs. Hence, combination of the serial plantation with substrate having high surface area is a potential strategy that can be used to improve the performance of CWs.},
}
@article {pmid33337106,
year = {2020},
author = {Fusco, V and Chieffi, D and Fanelli, F and Logrieco, AF and Cho, GS and Kabisch, J and Böhnlein, C and Franz, CMAP},
title = {Microbial quality and safety of milk and milk products in the 21st century.},
journal = {Comprehensive reviews in food science and food safety},
volume = {19},
number = {4},
pages = {2013-2049},
doi = {10.1111/1541-4337.12568},
pmid = {33337106},
issn = {1541-4337},
support = {H2020-E.U.3.2-678781//European Community's Horizon 2020/ ; //Mycokey/ ; //NextMilQ/ ; },
abstract = {Milk and milk products have been utilized by humans for many thousands of years. With the advent of metagenomic studies, our knowledge on the microbiota of milk and milk products, especially as affected by the environment, production, and storage parameters, has increased. Milk quality depends on chemical parameters (fat and protein content and absence of inhibitory substances), as well as microbial and somatic cells counts, and affects the price of milk. The effects of hygiene and effective cooling on the spoilage microbiota have shown that proteolytic and lipolytic bacteria such as Pseudomonas or Acinetobacter spp. predominate the spoilage bacterial populations. These bacteria can produce heat-stable proteases and lipases, which remain active after pasteurization and thus can spoil the milk during prolonged storage. Additionally, milk can become contaminated after pasteurization and therefore there is still a high demand on developing better cleaning and sanitation regimes and equipment, as well as test systems to (quantitatively) detect relevant pathogenic or spoilage microorganisms. Raw milk and raw milk cheese consumption is also increasing worldwide with the growing demand of minimally processed, sustainable, healthy, and local foods. In this context, emerging and re-emerging pathogens once again represent a major food safety challenge. As a result of global warming, it is conceivable that not only microbiological risks but also chemical risks relating to presence of mycotoxins or plant toxins in milk will increase. Herein, we provide an overview of the major microbial hazards occurring in the 21st century.},
}
@article {pmid33336444,
year = {2020},
author = {Donhauser, J and Qi, W and Bergk-Pinto, B and Frey, B},
title = {High temperatures enhance the microbial genetic potential to recycle C and N from necromass in high-mountain soils.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.15492},
pmid = {33336444},
issn = {1365-2486},
abstract = {Climate change is strongly affecting high-mountain soils and warming in particular is associated with pronounced changes in microbe-mediated C and N cycling, affecting plant-soil interactions and greenhouse gas balances and therefore feedbacks to global warming. We used shotgun metagenomics to assess changes in microbial community structures, as well as changes in microbial C- and N-cycling potential and stress response genes and we linked this data with changes in soil C and N pools and temperature-dependent measurements of bacterial growth rates. We did so by incubating high-elevation soil from the Swiss Alps at 4°C, 15°C, 25°C or 35°C for one month. We found no shift with increasing temperature in the C-substrate-degrader community towards taxa more capable of degrading recalcitrant organic matter. Conversely, at 35°C, we found an increase in genes associated with the degradation and modification of microbial cell walls, together with high bacterial growth rates. Together, these findings suggest that the rapidly growing high-temperature community is fueled by necromass from heat-sensitive taxa. This interpretation was further supported by a shift in the microbial N-cycling potential towards N mineralization and assimilation under higher temperatures, along with reduced potential for conversions among inorganic N forms. Microbial stress-response genes reacted inconsistently to increasing temperature, suggesting that the high-temperature community was not severely stressed by these conditions. Rather, soil microbes were able to acclimate by changing the thermal properties of membranes and cell walls as indicated by an increase in genes involved in membrane and cell wall modifications as well as a shift in the optimum temperature for bacterial growth towards the treatment temperature. Overall, our results suggest that high temperatures, as they may occur with heat waves under global warming, promote a highly active microbial community capable of rapid mineralization of microbial necromass, which may transiently amplify warming effects.},
}
@article {pmid33335687,
year = {2020},
author = {Altamirano, Á and Saa, PA and Garrido, D},
title = {Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {3897-3904},
pmid = {33335687},
issn = {2001-0370},
abstract = {The human gut hosts a complex community of microorganisms that directly influences gastrointestinal physiology, playing a central role in human health. Because of its importance, the metabolic interplay between the gut microbiome and host metabolism has gained special interest. While there has been great progress in the field driven by metagenomics and experimental studies, the mechanisms underpinning microbial composition and interactions in the microbiome remain poorly understood. Genome-scale metabolic models are mathematical structures capable of describing the metabolic potential of microbial cells. They are thus suitable tools for probing the metabolic properties of microbial communities. In this review, we discuss the most recent and relevant genome-scale metabolic modelling tools for inferring the composition, interactions, and ultimately, biological function of the constituent species of a microbial community with special emphasis in the gut microbiota. Particular attention is given to constraint-based metabolic modelling methods as well as hybrid agent-based methods for capturing the interactions and behavior of the community in time and space. Finally, we discuss the challenges hindering comprehensive modelling of complex microbial communities and its application for the in-silico design of microbial consortia with therapeutic functions.},
}
@article {pmid33335520,
year = {2020},
author = {Fang, X and Mei, Q and Fan, X and Zhu, C and Yang, T and Zhang, L and Geng, S and Pan, A},
title = {Diagnostic Value of Metagenomic Next-Generation Sequencing for the Detection of Pathogens in Bronchoalveolar Lavage Fluid in Ventilator-Associated Pneumonia Patients.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {599756},
pmid = {33335520},
issn = {1664-302X},
abstract = {Objective: To evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) in patients with ventilator-associated pneumonia (VAP). Methods: BALF samples of 72 patients with VAP were collected from August 2018 to May 2020. The diagnostic performance of conventional testing (CT) and mNGS methods were compared based on bacterial and fungal examinations. The diagnostic value of mNGS for viral and mixed infections was also analyzed. Results: The percentage of mNGS positive samples was significantly higher than that estimated by the CT method [odds ratio (OR), 4.33; 95% confidence interval (CI), 1.78-10.53; p < 0.001]. The sensitivity and specificity of mNGS for bacterial detection were 97.1% (95% CI, 93.2-101.0%) and 42.1% (95 CI, 30.7-53.5%), respectively, whereas the positive predictive value (PPV) and the negative predictive value (NPV) were 60.0% (95% CI, 48.7-71.3%) and 94.1% (95% CI, 88.7-99.6%), respectively. A total of 38 samples were negative for bacterial detection as determined by the CT method, while 22 samples were positive as shown by the mNGS method. Conflicting results were obtained for three samples between the two methods of bacterial detection. However, no significant differences were noted between the mNGS and CT methods (OR, 1.42; 95% CI, 0.68-2.97; p = 0.46) with regard to fungal infections. The sensitivity and specificity of mNGS were 71.9% (95% CI, 61.5-82.3%) and 77.5% (95% CI, 67.9-87.1%), respectively. mNGS exhibited a PPV of 71.9% (95% CI, 61.5-82.3%) and an NPV of 77.5% (95% CI, 67.9-87.1%). A total of 9 out of 40 samples were found positive for fungi according to mNGS, whereas the CT method failed to present positive results in these samples. The mNGS and CT methods produced conflicting results with regard to fungal detection of the two samples. A total of 30 patients were virus-positive using mNGS. Furthermore, 42 patients (58.3%) were identified as pulmonary mixed infection cases. Conclusions: mNGS detection using BALF improved the sensitivity and specificity of bacterial identification in patients who developed VAP. In addition, mNGS exhibited apparent advantages in detecting viruses and identifying mixed infections.},
}
@article {pmid33335515,
year = {2020},
author = {Luqman, A and Zabel, S and Rahmdel, S and Merz, B and Gruenheit, N and Harter, J and Nieselt, K and Götz, F},
title = {The Neuromodulator-Encoding sadA Gene Is Widely Distributed in the Human Skin Microbiome.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {573679},
pmid = {33335515},
issn = {1664-302X},
abstract = {Trace amines (TA) are endogenously produced in mammals, have a low concentration in the central nervous system (CNS), but trigger a variety of neurological effects and intervene in host cell communication. It emerged that neurotransmitters and TA are produced also by the microbiota. As it has been shown that TA contribute to wound healing, we examined the skin microbiome of probands using shotgun metagenomics. The phyla Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were predominant. Since SadA is a highly promiscuous TA-producing decarboxylase in Firmicutes, the skin microbiome was specifically examined for the presence of sadA-homologous genes. By mapping the reads of certain genes, we found that, although there were less reads mapping to sadA than to ubiquitous housekeeping genes (arcC and mutS), normalized reads counts were still >1000 times higher than those of rare control genes (icaA, icaB, and epiA). At protein sequence level SadA homologs were found in at least 7 phyla: Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and Cyanobacteria, and in 23 genera of the phylum Firmicutes. A high proportion of the genera that have a SadA homolog belong to the classical skin and intestinal microbiota. The distribution of sadA in so many different phyla illustrates the importance of horizontal gene transfer (HGT). We show that the sadA gene is widely distributed in the human skin microbiome. When comparing the sadA read counts in the probands, there was no correlation between age and gender, but an enormous difference in the sadA read counts in the microbiome of the individuals. Since sadA is involved in TA synthesis, it is likely that the TA content of the skin is correlated with the amount of TA producing bacteria in the microbiome. In this way, the microbiome-generated TA could influence signal transmission in the epithelial and nervous system.},
}
@article {pmid33335272,
year = {2020},
author = {Vibin, J and Chamings, A and Klaassen, M and Alexandersen, S},
title = {Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {22284},
pmid = {33335272},
issn = {2045-2322},
abstract = {Birds, notably wild ducks, are reservoirs of pathogenic and zoonotic viruses such as influenza viruses and coronaviruses. In the current study, we used metagenomics to detect and characterise avian DNA and RNA viruses from wild Pacific black ducks, Chestnut teals and Grey teals collected at different time points from a single location. We characterised a likely new species of duck aviadenovirus and a novel duck gyrovirus. We also report what, to the best of our knowledge, is the first finding of an avian orthoreovirus from Pacific black ducks and a rotavirus F from Chestnut teals. Other viruses characterised from the samples from these wild ducks belong to the virus families Astroviridae, Caliciviridae and Coronaviridae. Some of the viruses may have potential cross-species transmissibility, while others indicated a wide genetic diversity of duck viruses within a genus. The study also showed evidence of potential transmission of viruses along the East Asian-Australasian Flyway; potentially facilitated by migrating shorebirds. The detection and characterisation of several avian viruses not previously described, and causing asymptomatic but potentially also symptomatic infections suggest the need for more virus surveillance studies for pathogenic and potential zoonotic viruses in wildlife reservoirs.},
}
@article {pmid33335179,
year = {2020},
author = {Delroisse, J and Van Wayneberghe, K and Flammang, P and Gillan, D and Gerbaux, P and Opina, N and Todinanahary, GGB and Eeckhaut, I},
title = {Epidemiology of a SKin Ulceration Disease (SKUD) in the sea cucumber Holothuria scabra with a review on the SKUDs in Holothuroidea (Echinodermata).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {22150},
pmid = {33335179},
issn = {2045-2322},
support = {299101409//Fonds De La Recherche Scientifique - FNRS/ ; 299101409//Fonds De La Recherche Scientifique - FNRS/ ; },
abstract = {Aquacultivated sea cucumbers often suffer from SKin Ulceration Diseases (SKUDs). SKUDs have been observed in six holothuroid species from nine countries. All SKUDs present a similar symptom-the skin ulceration-and can be induced by bacteria, viruses, or abiotic factors. We here provide an update on SKUDs in holothuroids and analyse the case of the SKUD observed in Holothuria scabra in Madagascar. Field observations revealed a seasonality of the disease (i.e. wintertime maximum peak). Morphological analyses of integument ulcers showed that sea cucumbers react by forming a collagen fibre plug. Metagenomic analyses revealed a higher proportion of Vibrionaceae (Gammaproteobacteria) in ulcers in comparison to the healthy integument of the same individuals. Experimental infection assays were performed with ulcer crude extracts and bacteria isolated from these extracts (e.g. Vibrio parahaemolyticus) but did not significantly induce skin ulceration. Our results suggest that the disease is not induced by a pathogen or, at the very least, that the pathogen is not found within the ulcers as the disease is not transmissible by contact. An initial cause of the SKUD in Madagascar might be the repeated and prolonged exposures to cold temperatures. Opportunistic bacteria could settle in the dermis of ulcerated individuals and promote the ulcer extension. We propose a general nomenclature for SKUDs based on the acronym of the disease, the affected sea cucumber species (e.g. Hs for Holothuria scabra), the concerned region using an ISO code 3166-2 (e.g. MG for Madagascar), the description date (e.g. 20 for the year 2020), and, when known, the inducing agent (first letter of the general taxon, b for bacteria, v for virus in currently known cases; a a if it is an abiotic inducing parameter; nothing if the inducing cause has not been precisely identified). The disease described in this work will be designated under the name SKUD Hs-MG-20.},
}
@article {pmid33334522,
year = {2021},
author = {Mao, G and Liang, J and Wang, Q and Zhao, C and Bai, Y and Liu, R and Liu, H and Qu, J},
title = {Epilithic biofilm as a reservoir for functional virulence factors in wastewater-dominant rivers after WWTP upgrade.},
journal = {Journal of environmental sciences (China)},
volume = {101},
number = {},
pages = {27-35},
doi = {10.1016/j.jes.2020.05.014},
pmid = {33334522},
issn = {1001-0742},
mesh = {Biofilms ; Ecosystem ; Humans ; RNA, Ribosomal, 16S/genetics ; *Rivers ; Virulence Factors ; *Waste Water ; },
abstract = {Virulence factors (VFs) confer upon pathogens the ability to cause various types of damage or diseases. Wastewater treatment plants (WWTPs) are important point sources for the emission of pathogens and VFs into receiving rivers. Conventional WWTP upgrades are often implemented to improve the water quality of receiving ecosystems. However, knowledge on the pathogens, VFs, and health risks to receiving aquatic ecosystems after upgrade remains limited. In this study, we investigated detailed pathogenic information, including taxa, pathogenicity, and health risk, in two wastewater-dominant rivers after WWTP upgrade. Using 16S rRNA gene sequencing, we screened 14 potential pathogens in water and epilithic biofilm samples, though they were significantly more enriched in the biofilms. Combining 16S rRNA and metagenomic sequencing data, we identified Pseudomonas and Aeromonas as the dominant pathogenic taxa carrying functional VFs (e.g., mobility and offensive) in the epilithic biofilm. Moreover, strong pathogen-specific VF-host co-occurrence events were observed in the epilithic biofilm samples, indicating the importance of biofilms as reservoirs and vehicles for VFs. Further, we demonstrated that mobility VF is crucial for biofilm formation and pathogens in biofilm carrying offensive VF may be highly invasive. Quantification and health risk assessment suggested that the skin contact risk of P. aeruginosa carrying VFs was higher than the acceptable probability of 10-4 in both water and epilithic biofilm samples, which may threaten ecological and human health.},
}
@article {pmid33334204,
year = {2020},
author = {Hasbun, R},
title = {Healthcare-associated ventriculitis: current and emerging diagnostic and treatment strategies.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/14787210.2021.1866544},
pmid = {33334204},
issn = {1744-8336},
abstract = {Introduction: Healthcare-associated ventriculitis and meningitis occur after neurosurgical procedures, is associated with an adverse outcome in the majority of patients and represent a diagnostic challenge to clinicians. As the cerebrospinal fluid (CSF) culture is the cornerstone of diagnosis, obtaining CSF studies prior to starting antibiotic therapy is key. Areas covered: This review will evaluate the incidence, risk factors, clinical presentation, diagnosis, empirical intravenous antibiotic therapy, adjunctive intrathecal therapy, microbiology, prognosis, and prevention of HCAVM. We highlight the challenges and limitations of the currently available diagnostic methods and definitions and explore novel technologies. Our review included the search for published literature until June 2020. Expert opinion: Despite available preventive measures, HCAVM continues to occur and to be independently associated with significant neurological morbidity and mortality in the majority of patients. The cornerstone of the diagnosis of HCAVM is a positive CSF culture but the microbiological yield is reduced to ~50% with prior antimicrobial therapy. Although the CSF profile is not affected by antibiotic therapy it has a fair diagnostic accuracy. Future research efforts should concentrate in identifying novel diagnostic tools such as polymerase chain reaction (PCR) or metagenomic sequencing.},
}
@article {pmid33333290,
year = {2020},
author = {Nagai, M and Okabayashi, T and Akagami, M and Matsuu, A and Fujimoto, Y and Hashem, MA and Mekata, H and Nakao, R and Matsuno, K and Katayama, Y and Oba, M and Omatsu, T and Asai, T and Nakagawa, K and Ito, H and Madarame, H and Kawai, K and Ito, T and Nonaka, N and Tsukiyama-Kohara, K and Inoshima, Y and Mizutani, T and Misawa, N},
title = {Metagenomic identification, sequencing, and genome analysis of porcine hepe-astroviruses (bastroviruses) in porcine feces inn Japan.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {104664},
doi = {10.1016/j.meegid.2020.104664},
pmid = {33333290},
issn = {1567-7257},
abstract = {Recently, hepe-astrovirus-like RNA viruses named bastroviruses (BastVs), have been found in human, pig, bat, and rat fecal samples. In this study, we determined nearly complete genome sequences of four BastVs in the feces of healthy pigs. Genetic characterization revealed that these porcine BastVs (PBastVs) and BastVs from other animals including humans, had the same genome organization, that is, they contained three predicted conserved domains of viral methyltransferase, RNA helicase, and RdRp in the nonstructural ORF1 and the astrovirus capsid domain in the structural ORF2. Phylogenetic analyses using RNA-dependent RNA polymerase and the capsid region revealed that PBastVs branched with bat and rat BastVs; however, the groups formed by each host were distantly related to human BastVs. Pairwise amino acid sequence comparison demonstrated that PBastVs shared 95.2-98.6% and 76.1-95.5% sequence identity among each other in the ORF1 and ORF2 regions, respectively; the sequence identities between PBastVs and BastVs from other animals were 21.4-42.5% and 9.1-20.6% in the ORF1 and ORF2 regions, respectively. This suggested that BastVs were derived from a common ancestor but evolved independently in each host population during a prolonged period. Putative recombination events were identified in the PBastV genome, suggesting that PBastVs gain sequence diversity and flexibility through recombination events. In an analysis of previously obtained metagenomic data, PBastV sequence reads were detected in 7.3% (23/315) of fecal samples from pigs indicating that PBastVs are distributed among pig populations in Japan.},
}
@article {pmid33332429,
year = {2020},
author = {Alex, CE and Fahsbender, E and Altan, E and Bildfell, R and Wolff, P and Jin, L and Black, W and Jackson, K and Woods, L and Munk, B and Tse, T and Delwart, E and Pesavento, PA},
title = {Viruses in unexplained encephalitis cases in American black bears (Ursus americanus).},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0244056},
pmid = {33332429},
issn = {1932-6203},
abstract = {Viral infections were investigated in American black bears (Ursus americanus) from Nevada and northern California with and without idiopathic encephalitis. Metagenomics analyses of tissue pools revealed novel viruses in the genera Circoviridae, Parvoviridae, Anelloviridae, Polyomaviridae, and Papillomaviridae. The circovirus and parvovirus were of particular interest due to their potential importance as pathogens. We characterized the genomes of these viruses and subsequently screened bears by PCR to determine their prevalence. The circovirus (Ursus americanus circovirus, UaCV) was detected at a high prevalence (10/16, 67%), and the chaphamaparvovirus (Ursus americanus parvovirus, UaPV) was found in a single bear. We showed that UaCV is present in liver, spleen/lymph node, and brain tissue of selected cases by in situ hybridization (ISH) and PCR. Infections were detected in cases of idiopathic encephalitis and in cases without inflammatory brain lesions. Infection status was not clearly correlated with disease, and the significance of these infections remains unclear. Given the known pathogenicity of a closely related mammalian circovirus, and the complex manifestations of circovirus-associated diseases, we suggest that UaCV warrants further study as a possible cause or contributor to disease in American black bears.},
}
@article {pmid33331849,
year = {2020},
author = {Scholz, GE and Linard, B and Romashchenko, N and Rivals, E and Pardi, F},
title = {Rapid screening and detection of inter-type viral recombinants using Phylo-K-Mers.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaa1020},
pmid = {33331849},
issn = {1367-4811},
abstract = {MOTIVATION: Novel recombinant viruses may have important medical and evolutionary significance, as they sometimes display new traits not present in the parental strains. This is particularly concerning when the new viruses combine fragments coming from phylogenetically-distinct viral types. Here, we consider the task of screening large collections of sequences for such novel recombinants. A number of methods already exist for this task. However, these methods rely on complex models and heavy computations that are not always practical for a quick scan of a large number of sequences.<br><br>RESULTS: We have developed SHERPAS, a new program to detect novel recombinants and provide a first estimate of their parental composition. Our approach is based on the precomputation of a large database of &quot;phylogenetically-informed k-mers&quot;, an idea recently introduced in the context of phylogenetic placement in metagenomics. Our experiments show that SHERPAS is hundreds to thousands of times faster than existing software, and enables the analysis of thousands of whole genomes, or long sequencing reads, within minutes or seconds, and with limited loss of accuracy.<br><br>The source code is freely available for download at https://github.com/phylo42/sherpas.<br><br>SUPPLEMENTARY INFORMATION: Supplementary Materials are available at Bioinformatics online.},
}
@article {pmid33331820,
year = {2020},
author = {Gregorova, M and Morse, D and Brignoli, T and Steventon, J and Hamilton, F and Albur, M and Arnold, D and Thomas, M and Halliday, A and Baum, H and Rice, C and Avison, MB and Davidson, AD and Santopaolo, M and Oliver, E and Goenka, A and Finn, A and Wooldridge, L and Amulic, B and Boyton, RJ and Altmann, DM and Butler, DK and McMurray, C and Stockton, J and Nicholls, S and Cooper, C and Loman, N and Cox, MJ and Rivino, L and Massey, RC},
title = {Post-acute COVID-19 associated with evidence of bystander T-cell activation and a recurring antibiotic-resistant bacterial pneumonia.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
doi = {10.7554/eLife.63430},
pmid = {33331820},
issn = {2050-084X},
support = {212258/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; MR/S019553/1//UKRI/ ; MR/R02622X/1//UKRI/ ; CF Trust SRC 015//Cystic Fibrosis Trust/ ; MR/S019553/1//UK Research and Innovation/ ; MR/R02622X/1//UK Research and Innovation/ ; },
abstract = {Here, we describe the case of a COVID-19 patient who developed recurring ventilator-associated pneumonia caused by Pseudomonas aeruginosa that acquired increasing levels of antimicrobial resistance (AMR) in response to treatment. Metagenomic analysis revealed the AMR genotype, while immunological analysis revealed massive and escalating levels of T-cell activation. These were both SARS-CoV-2 and P. aeruginosa specific, and bystander activated, which may have contributed to this patient's persistent symptoms and radiological changes.},
}
@article {pmid33330938,
year = {2020},
author = {Damhorst, GL and Adelman, MW and Woodworth, MH and Kraft, CS},
title = {Current capabilities of gut microbiome-based diagnostics and the promise of clinical application.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaa689},
pmid = {33330938},
issn = {1537-6613},
}
@article {pmid33330904,
year = {2020},
author = {Thänert, R and Keen, EC and Dantas, G and Warner, BB and Tarr, PI},
title = {Necrotizing enterocolitis and the microbiome: Current status and future directions.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaa604},
pmid = {33330904},
issn = {1537-6613},
abstract = {Decades of research have failed to define the pathophysiology of necrotizing enterocolitis (NEC), a devastating pediatric gastrointestinal disorder of preterm infants. However, recent evidence suggests that host-microbiota interactions, in which microbial dysbiosis is followed by loss of barrier integrity, inflammation, and necrosis, are central to NEC development. Thus, greater knowledge of the preterm infant microbiome could accelerate attempts to diagnose, treat, and prevent NEC. Here, we summarize clinical characteristics of and risk factors for NEC, the structure of the pre-event NEC microbiome, how this community interfaces with host immunology, and microbiome-based approaches that might prevent or lessen the severity of NEC in this very vulnerable population.},
}
@article {pmid33330625,
year = {2020},
author = {Qiu, Q and Wang, J and Yan, Y and Roy, B and Chen, Y and Shang, X and Dou, T and Han, L},
title = {Metagenomic Analysis Reveals the Distribution of Antibiotic Resistance Genes in a Large-Scale Population of Healthy Individuals and Patients With Varied Diseases.},
journal = {Frontiers in molecular biosciences},
volume = {7},
number = {},
pages = {590018},
pmid = {33330625},
issn = {2296-889X},
abstract = {The human gut microbiome is a reservoir for antibiotic resistance gene (ARG). Therefore, characterizing resistome distribution and potential disease markers can help manage antibiotics at the clinical level. While much population-level research has highlighted the strong effect of donor geographic origin on ARG prevalence in the human gut, little is known regarding the effects of other properties, such as age, sex, and disease. Here we employed 2,037 fecal metagenomes from 12 countries. By quantifying the known resistance genes for 24 types of antibiotics in each community, we showed that tetracycline, aminoglycoside, beta-lactam, macrolide-lincosamide-streptogramin (MLS), and vancomycin resistance genes were the dominant ARG types in the human gut. We then compared the ARG profiles of 1427 healthy individuals from the 2,037 samples and observed significant differences across countries. This was consistent with expectations that regional antibiotic usage and exposure in medical and food production contexts affect distribution. Although no specific uniform pattern of ARG was observed, a significant increase in resistance potential among multiple disease groups implied that the disease condition may be another source of ARG variance. In particular, the co-occurrence pattern of some enriched bacterial species and ARGs that were obtained in type 2 diabetes (T2D) and liver cirrhosis patients implied that some disease-associated species may be potential hosts of enriched ARGs, which could be potential biomarkers for the prediction and intervention of such diseases. Overall, our study identifies factors associated with the human gut resistome, including substantial effects of region and heterogeneous effects of disease status, and highlights the value of ARG analysis in disease research and clinical applications.},
}
@article {pmid33329686,
year = {2020},
author = {Abdala Asbun, A and Besseling, MA and Balzano, S and van Bleijswijk, JDL and Witte, HJ and Villanueva, L and Engelmann, JC},
title = {Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results.},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {489357},
pmid = {33329686},
issn = {1664-8021},
abstract = {Marker gene sequencing of the rRNA operon (16S, 18S, ITS) or cytochrome c oxidase I (CO1) is a popular means to assess microbial communities of the environment, microbiomes associated with plants and animals, as well as communities of multicellular organisms via environmental DNA sequencing. Since this technique is based on sequencing a single gene, or even only parts of a single gene rather than the entire genome, the number of reads needed per sample to assess the microbial community structure is lower than that required for metagenome sequencing. This makes marker gene sequencing affordable to nearly any laboratory. Despite the relative ease and cost-efficiency of data generation, analyzing the resulting sequence data requires computational skills that may go beyond the standard repertoire of a current molecular biologist/ecologist. We have developed Cascabel, a scalable, flexible, and easy-to-use amplicon sequence data analysis pipeline, which uses Snakemake and a combination of existing and newly developed solutions for its computational steps. Cascabel takes the raw data as input and delivers a table of operational taxonomic units (OTUs) or Amplicon Sequence Variants (ASVs) in BIOM and text format and representative sequences. Cascabel is a highly versatile software that allows users to customize several steps of the pipeline, such as selecting from a set of OTU clustering methods or performing ASV analysis. In addition, we designed Cascabel to run in any linux/unix computing environment from desktop computers to computing servers making use of parallel processing if possible. The analyses and results are fully reproducible and documented in an HTML and optional pdf report. Cascabel is freely available at Github: https://github.com/AlejandroAb/CASCABEL.},
}
@article {pmid33329483,
year = {2020},
author = {Haddad, G and Bellali, S and Fontanini, A and Francis, R and La Scola, B and Levasseur, A and Bou Khalil, J and Raoult, D},
title = {Rapid Scanning Electron Microscopy Detection and Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2 and Other Respiratory Viruses.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {596180},
pmid = {33329483},
issn = {1664-302X},
abstract = {There is an urgent need for accurate and rapid testing methods to quickly identify infected patients as well as asymptomatic carriers, in order to prevent the spread of emerging viruses. Here, we developed a rapid testing strategy by scanning electron microscopy capable of detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses directly from patients. We evaluated our results by comparing them to real-time reverse transcription-polymerase chain reaction (RT-PCR) and metagenomic sequencing results. We correlated the presence of the SARS-CoV-2 to the viral load, where samples with Ct values lower than 18 were all detected by scanning electron microscopy (SEM). The sensitivity deacresed progressively with higher Ct values. In addition, we found a correlation with metagenomic sequencing, where all samples detected by SEM were sequenced and viral sequences were easily recovered. Following this study, SEM proved its efficiency as a frontline method for directly detecting previously unknown microorganisms that cannot be targeted by molecular methods and can cause potential outbreaks.},
}
@article {pmid33329463,
year = {2020},
author = {Long, C and Venema, K},
title = {Pretreatment of Rapeseed Meal Increases Its Recalcitrant Fiber Fermentation and Alters the Microbial Community in an in vitro Model of Swine Large Intestine.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {588264},
pmid = {33329463},
issn = {1664-302X},
abstract = {The aim of current study was to investigate in an in vitro study how enzymatic and chemical pretreated rapeseed meal (RSM) influences the fiber fermentation and microbial community in the swine large intestine. RSM was processed enzymatically by a cellulase (CELL), two pectinases (PECT), or chemically by an alkaline (ALK) treatment. 16S rRNA gene sequencing data was performed to evaluate changes in the gut microbiota composition, whereas short-chain fatty acid (SCFA) production (ion-chromatography) and non-starch polysaccharides (NSP) composition (using monoclonal antibodies; mAbs) were used to assess fiber degradation. The results showed that ALK, CELL, PECT1, and PECT2 changed microbial community composition, increased the predicted abundance of microbial fiber-degrading enzymes and pathways, and increased acetic acid, propionic acid, butyric acid, and total SCFA production. The increased microbial genera positively correlated with SCFA production. Monoclonal antibody analyses showed that the cell wall polysaccharide structures of RSM shifted after ALK, CELL, PECT1, and PECT2 treatment. The degradation of NSP during the fermentation period was dynamic, and not continuous based on the epitope recognition by mAbs. This study provides the first detailed analysis of changes in the swine intestinal microbiota due to RSM modified by ALK, CELL, PECT1, and PECT2, which altered the microbial community structure, shifted the predicted functional metagenomic profile and subsequently increased total SCFA production. Our findings that ALK, CELL, PECT1, and PECT2 increased fiber degradability in RSM could help guide feed additive strategies to improve efficiency and productivity in swine industry. The current study gave insight into how enzymatic treatment of feed can alter microbial communities, which provides good opportunity to develop novel carbohydrase treatments, particularly in swine feed.},
}
@article {pmid33329461,
year = {2020},
author = {Yu, J and Pavia, MJ and Deem, LM and Crow, SE and Deenik, JL and Penton, CR},
title = {DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {587972},
pmid = {33329461},
issn = {1664-302X},
abstract = {The functions and interactions of individual microbial populations and their genes in agricultural soils amended with biochar remain elusive but are crucial for a deeper understanding of nutrient cycling and carbon (C) sequestration. In this study, we coupled DNA stable isotope probing (SIP) with shotgun metagenomics in order to target the active community in microcosms which contained soil collected from biochar-amended and control plots under napiergrass cultivation. Our analyses revealed that the active community was composed of high-abundant and low-abundant populations, including Actinobacteria, Proteobacteria, Gemmatimonadetes, and Acidobacteria. Although biochar did not significantly shift the active taxonomic and functional communities, we found that the narG (nitrate reductase) gene was significantly more abundant in the control metagenomes. Interestingly, putative denitrifier genomes generally encoded one gene or a partial denitrification pathway, suggesting denitrification is typically carried out by an assembly of different populations within this Oxisol soil. Altogether, these findings indicate that the impact of biochar on the active soil microbial community are transient in nature. As such, the addition of biochar to soils appears to be a promising strategy for the long-term C sequestration in agricultural soils, does not impart lasting effects on the microbial functional community, and thus mitigates un-intended microbial community shifts that may lead to fertilizer loss through increased N cycling.},
}
@article {pmid33329454,
year = {2020},
author = {Park, S and Steinegger, M and Cho, HS and Chun, J},
title = {Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {585622},
pmid = {33329454},
issn = {1664-302X},
abstract = {Limosilactobacillus reuteri is a model symbiont that colonizes the guts of vertebrates in studies on host adaptation of the gut symbiont. Previous studies have investigated host-specific phylogenetic and functional properties by isolating the genomic sequence. This dependency on genome isolation is a significant bottleneck. Here, we propose a method to study the association between L. reuteri and its hosts directly from metagenomic reads without strain isolation using pan-genomes. We characterized the host-specificity of L. reuteri in metagenomic samples, not only in previously studied organisms (mice and pigs) but also in dogs. For each sample, two types of profiles were generated: (1) genome-based strain type abundance profiles and (2) gene composition profiles. Our profiles showed host-association of L. reuteri in both phylogenetic and functional aspects without depending on host-specific genome isolation. We observed not only the presence of host-specific lineages, but also the dominant lineages associated with the different hosts. Furthermore, we showed that metagenome-assembled genomes provide detailed insights into the host-specificity of L. reuteri. We inferred evolutionary trajectories of host-associative L. reuteri strains in the metagenomic samples by placing the metagenome-assembled genomes into a phylogenetic tree and identified novel host-specific genes that were unannotated in existing pan-genome databases. Our pan-genomic approach reduces the need for time-consuming and expensive host-specific genome isolation, while producing consistent results with previous host-association findings in mice and pigs. Additionally, we predicted associations that have not yet been studied in dogs.},
}
@article {pmid33329438,
year = {2020},
author = {Wu, X and Shang, Y and Wei, Q and Chen, J and Zhang, H and Chen, Y and Gao, X and Wang, Z and Zhang, H},
title = {Gut Microbiota in Dholes During Estrus.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {575731},
pmid = {33329438},
issn = {1664-302X},
abstract = {The co-evolution of gut microbes and the host plays a vital role in the survival and reproduction of the host. The dhole (Cuon alpinus) has been listed as endangered species by the International Union for Conservation of Nature; therefore, conservation and effective breeding of dholes are essential. Effective estrus can promote reproduction. However, little is known about the relative contribution of estrus in shaping the structure and the functions of fecal microbiota. Here, we investigated the potential association between estrus and the fecal microbiota in dholes using shotgun metagenomic sequencing. We found that the estrus stages in dholes vary significantly in terms of gut bacterial composition and microbiome metabolism and function. Compared with that of non-estrus, adult dholes, the microbiome of estrus adult dholes had a significantly higher abundance of Bacillus faecalis and Veillonella, which play a key role in the synthesis of sex hormones and nucleic acids, energy production, and reproductive cell division. The insulin and energy metabolism-related pathways are significantly enhanced in the gut microbes and the related gluconeogenic enzymes are significantly enriched during estrus. These findings suggest that the structure and metagenome of the fecal microbiome during estrus have a significant effect in promoting estrus in dholes, thus providing a new perspective for dhole conservation.},
}
@article {pmid33328652,
year = {2020},
author = {McAllister, SM and Vandzura, R and Keffer, JL and Polson, SW and Chan, CS},
title = {Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {33328652},
issn = {1751-7370},
support = {OCE-1155290//National Science Foundation (NSF)/ ; N00014-17-1-2640//United States Department of Defense | United States Navy | Office of Naval Research (ONR)/ ; NNX10AN63H/NASA/NASA/United States ; Dissertation Fellowship//University of Delaware (UD)/ ; },
abstract = {In principle, iron oxidation can fuel significant primary productivity and nutrient cycling in dark environments such as the deep sea. However, we have an extremely limited understanding of the ecology of iron-based ecosystems, and thus the linkages between iron oxidation, carbon cycling, and nitrate reduction. Here we investigate iron microbial mats from hydrothermal vents at Lō'ihi Seamount, Hawai'i, using genome-resolved metagenomics and metatranscriptomics to reconstruct potential microbial roles and interactions. Our results show that the aerobic iron-oxidizing Zetaproteobacteria are the primary producers, concentrated at the oxic mat surface. Their fixed carbon supports heterotrophs deeper in the mat, notably the second most abundant organism, Candidatus Ferristratum sp. (uncultivated gen. nov.) from the uncharacterized DTB120 phylum. Candidatus Ferristratum sp., described using nine high-quality metagenome-assembled genomes with similar distributions of genes, expressed nitrate reduction genes narGH and the iron oxidation gene cyc2 in situ and in response to Fe(II) in a shipboard incubation, suggesting it is an anaerobic nitrate-reducing iron oxidizer. Candidatus Ferristratum sp. lacks a full denitrification pathway, relying on Zetaproteobacteria to remove intermediates like nitrite. Thus, at Lō'ihi, anaerobic iron oxidizers coexist with and are dependent on aerobic iron oxidizers. In total, our work shows how key community members work together to connect iron oxidation with carbon and nitrogen cycling, thus driving the biogeochemistry of exported fluids.},
}
@article {pmid33328537,
year = {2020},
author = {Seferovic, MD and Mohammad, M and Pace, RM and Engevik, M and Versalovic, J and Bode, L and Haymond, M and Aagaard, KM},
title = {Maternal diet alters human milk oligosaccharide composition with implications for the milk metagenome.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {22092},
pmid = {33328537},
issn = {2045-2322},
support = {R01HD091731/NH/NIH HHS/United States ; },
abstract = {Human milk is the optimal nutrition source for infants, and oligosaccharides represent the third most abundant component in milk after lactose and fat. Human milk oligosaccharides (HMO) are favorable macromolecules which are, interestingly, indigestible by the infant but serve as substrates for bacteria. Hypothesizing that the maternal diet itself might influence HMO composition, we sought to directly determine the effect maternal diet on HMO and the milk bacteria. Employing a human cross-over study design, we demonstrate that distinct maternal dietary carbohydrate and energy sources preferentially alter milk concentrations of HMO, including fucosylated species. We find significant associations between the concentration of HMO-bound fucose and the abundance of fucosidase (a bacterial gene that digests fucose moieties) harbored by milk bacteria. These studies reveal a successive mechanism by which the maternal diet during lactation alters milk HMO composition, which in turn shapes the functional milk microbiome prior to infant ingestion.},
}
@article {pmid33328359,
year = {2020},
author = {Agrawal, S and Orschler, L and Sinn, J and Lackner, S},
title = {High-throughput profiling of antibiotic resistance genes in wastewater: comparison between a pond system in Namibia and an activated sludge treatment in Germany.},
journal = {Journal of water and health},
volume = {18},
number = {6},
pages = {867-878},
doi = {10.2166/wh.2020.018},
pmid = {33328359},
issn = {1477-8920},
mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Germany ; Namibia ; Ponds ; *Sewage ; *Waste Water ; },
abstract = {There are increasing concerns about wastewater treatment plants (WWTPs) acting as hotspots for antibiotic resistance genes (ARG). However, their role largely depends upon the treatment methods and antibiotics in the wastewater. To better understand these influences, we compared the occurrence and fate of ARG between a pond system in a developing country (Namibia) and an advanced WWTP (activated sludge system) in a developed country (Germany). A targeted metagenomic approach was used to investigate the wide-spectrum profiles of ARGs and their co-occurrence patterns at both locations. In total, 93 ARG subtypes were found in the German influent wastewater, 277 in the Namibian influent wastewater. The abundant ARG types found in Namibia and Germany differed, especially for multidrug resistance genes. The differences in occurrence and reduction can help to understand the performance of simple WWTP such as pond systems common in Namibia, where direct contact with wastewater is a potential risk for contamination.},
}
@article {pmid33328245,
year = {2020},
author = {Masi, AC and Embleton, ND and Lamb, CA and Young, G and Granger, CL and Najera, J and Smith, DP and Hoffman, KL and Petrosino, JF and Bode, L and Berrington, JE and Stewart, CJ},
title = {Human milk oligosaccharide DSLNT and gut microbiome in preterm infants predicts necrotising enterocolitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2020-322771},
pmid = {33328245},
issn = {1468-3288},
abstract = {OBJECTIVE: Necrotising enterocolitis (NEC) is a devastating intestinal disease primarily affecting preterm infants. The underlying mechanisms are poorly understood: mother's own breast milk (MOM) is protective, possibly relating to human milk oligosaccharide (HMO) and infant gut microbiome interplay. We investigated the interaction between HMO profiles and infant gut microbiome development and its association with NEC.<br><br>DESIGN: We performed HMO profiling of MOM in a large cohort of infants with NEC (n=33) with matched controls (n=37). In a subset of 48 infants (14 with NEC), we also performed longitudinal metagenomic sequencing of infant stool (n=644).<br><br>RESULTS: Concentration of a single HMO, disialyllacto-N-tetraose (DSLNT), was significantly lower in MOM received by infants with NEC compared with controls. A MOM threshold level of 241 nmol/mL had a sensitivity and specificity of 0.9 for NEC. Metagenomic sequencing before NEC onset showed significantly lower relative abundance of Bifidobacterium longum and higher relative abundance of Enterobacter cloacae in infants with NEC. Longitudinal development of the microbiome was also impacted by low MOM DSLNT associated with reduced transition into preterm gut community types dominated by Bifidobacterium spp and typically observed in older infants. Random forest analysis combining HMO and metagenome data before disease accurately classified 87.5% of infants as healthy or having NEC.<br><br>CONCLUSION: These results demonstrate the importance of HMOs and gut microbiome in preterm infant health and disease. The findings offer potential targets for biomarker development, disease risk stratification and novel avenues for supplements that may prevent life-threatening disease.},
}
@article {pmid33328144,
year = {2020},
author = {Kolmeder, CA and de Vos, WM},
title = {Roadmap to functional characterization of the human intestinal microbiota in its interaction with the host.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {},
number = {},
pages = {113751},
doi = {10.1016/j.jpba.2020.113751},
pmid = {33328144},
issn = {1873-264X},
abstract = {It is known for more than 100 years that the intestinal microbes are important for the host's health and the last decade this is being intensely studied with a focus on the mechanistic aspects. Among the fundamental functions of the intestinal microbiome are the priming of the immune system, the production of essential vitamins and the energy harvest from foods. By now, several dozens of diseases, both intestinal and non-intestinal related, have been associated with the intestinal microbiome. Initially, this was based on the description of the composition between groups of different health status or treatment arms based on phylogenetic approaches based on the 16S rRNA gene sequences. This way of analysis has mostly moved to the analysis of all the genes or transcripts of the microbiome i.e. metagenomics and meta-transcriptomics. Differences are regularly found but these have to be taken with caution as we still do not know what the majority of genes of the intestinal microbiome are capable of doing. To circumvent this caveat researchers are studying the proteins and the metabolites of the microbiome and the host via metaproteomics and metabolomics approaches. However, also here the complexity is high and only a fraction of signals obtained with high throughput instruments can be identified and assigned to a known protein or molecule. Therefore, modern microbiome research needs advancement of existing and development of new analytical techniques. The usage of model systems like intestinal organoids where samples can be taken and processed rapidly as well as microfluidics systems may help. This review aims to elucidate what we know about the functionality of the human intestinal microbiome, what technologies are advancing this knowledge, and what innovations are still required to further evolve this actively developing field.},
}
@article {pmid33327517,
year = {2020},
author = {Menaa, F and Wijesinghe, PAUI and Thiripuranathar, G and Uzair, B and Iqbal, H and Khan, BA and Menaa, B},
title = {Ecological and Industrial Implications of Dynamic Seaweed-Associated Microbiota Interactions.},
journal = {Marine drugs},
volume = {18},
number = {12},
pages = {},
pmid = {33327517},
issn = {1660-3397},
abstract = {Seaweeds are broadly distributed and represent an important source of secondary metabolites (e.g., halogenated compounds, polyphenols) eliciting various pharmacological activities and playing a relevant ecological role in the anti-epibiosis. Importantly, host (as known as basibiont such as algae)-microbe (as known as epibiont such as bacteria) interaction (as known as halobiont) is a driving force for coevolution in the marine environment. Nevertheless, halobionts may be fundamental (harmless) or detrimental (harmful) to the functioning of the host. In addition to biotic factors, abiotic factors (e.g., pH, salinity, temperature, nutrients) regulate halobionts. Spatiotemporal and functional exploration of such dynamic interactions appear crucial. Indeed, environmental stress in a constantly changing ocean may disturb complex mutualistic relations, through mechanisms involving host chemical defense strategies (e.g., secretion of secondary metabolites and antifouling chemicals by quorum sensing). It is worth mentioning that many of bioactive compounds, such as terpenoids, previously attributed to macroalgae are in fact produced or metabolized by their associated microorganisms (e.g., bacteria, fungi, viruses, parasites). Eventually, recent metagenomics analyses suggest that microbes may have acquired seaweed associated genes because of increased seaweed in diets. This article retrospectively reviews pertinent studies on the spatiotemporal and functional seaweed-associated microbiota interactions which can lead to the production of bioactive compounds with high antifouling, theranostic, and biotechnological potential.},
}
@article {pmid33326896,
year = {2020},
author = {Wu, Z and Nguyen, D and Lam, TYC and Zhuang, H and Shrestha, S and Raskin, L and Khanal, SK and Lee, PH},
title = {Synergistic association between cytochrome bd-encoded Proteiniphilum and reactive oxygen species (ROS)-scavenging methanogens in microaerobic-anaerobic digestion of lignocellulosic biomass.},
journal = {Water research},
volume = {190},
number = {},
pages = {116721},
doi = {10.1016/j.watres.2020.116721},
pmid = {33326896},
issn = {1879-2448},
abstract = {Intermittent (every other day) microaerobic [picomolar oxygen by oxidation-reduction potential (ORP) set at +25 mV above anaerobic baseline] digestion of lignocellulosic biomass showed higher digestibility and better stability at a high organic loading rate (OLR) of 5 g volatile solids (VS)/L/d than that under strict anaerobic conditions. However, the microbial mechanisms supporting the delicate balance under microaeration remain underexplored. On the basis of our previous findings that microbial communities in replicate experiments were dominated by strains of the genus Proteiniphilum but contained diverse taxa of methanogenic archaea, here we recovered related genomes and reconstructed the putative metabolic pathways using a genome-centric metagenomic approach. The highly enriched Proteiniphilum strains were identified as efficient cellulolytic facultative bacterium, which directly degraded lignocellulose to carbon dioxide, formate, and acetate via aerobic respiration and anaerobic fermentation, alternatively. Moreover, high oxygen affinity cytochromes, bd-type terminal oxidases, in Proteiniphilum strains were found to be closely associated with such picomolar oxygen conditions, which has long been overlooked in anaerobic digestion. Furthermore, hydrogenotrophic methanogenesis was the prevalent pathway for methane production while Methanosarcina, Methanobrevibacter, and Methanocorpusculum were the dominant methanogens in the replicate experiments. Importantly, the two functional groups, namely cellulolytic facultative Proteiniphilum strains and methanogens, encoded various antioxidant enzymes. Energy-dependent reactive oxygen species (ROS) scavengers (superoxide reductase (SOR) and rubrerythrin (rbr) were ubiquitously present in different methanogenic taxa in response to replicate-specific ORP levels (-470, -450 and -475 mV). Collectively, cytochrome bd oxidase and ROS defenders may play roles in improving the digestibility and stability observed in intermittent microaerobic digestion.},
}
@article {pmid33326581,
year = {2020},
author = {Anthony, WE and Burnham, CD and Dantas, G and Kwon, JH},
title = {The Gut Microbiome as a Reservoir for Antimicrobial Resistance.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaa497},
pmid = {33326581},
issn = {1537-6613},
abstract = {This review will discuss the gut as a reservoir for antimicrobial resistance, colonization resistance, and how disruption of the microbiome can lead to colonization by pathogenic organisms. There is a focus on the gut as a reservoir for β-lactam and plasmid mediated quinolone resistance. Finally, the role of functional metagenomics and long read sequencing technologies to detect and understand antimicrobial resistance genes within the gut microbiome, and the potential for future microbiome-directed methods to detect and prevent infection is discussed.},
}
@article {pmid33326438,
year = {2020},
author = {Schwabl, P and Maiguashca Sánchez, J and Costales, JA and Ocaña-Mayorga, S and Segovia, M and Carrasco, HJ and Hernández, C and Ramírez, JD and Lewis, MD and Grijalva, MJ and Llewellyn, MS},
title = {Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity.},
journal = {PLoS genetics},
volume = {16},
number = {12},
pages = {e1009170},
pmid = {33326438},
issn = {1553-7404},
abstract = {Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obligate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Modern sequence capture methods enable pathogen genetic variation to be analyzed directly from host/vector material but are often too complex and expensive for resource-poor settings where infectious diseases prevail. This study proposes a simple, cost-effective 'genome-wide locus sequence typing' (GLST) tool based on massive parallel amplification of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding completes library preparation at under 4 USD per sample. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metagenomic extracts from triatomine vectors containing a minimum of 3.69 pg/μl T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, TcV and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic distances at regional (< 150 km) as well as continental scales. The markers also clearly separate TcI, TcIII, TcIV and TcV + TcVI and appear to distinguish multiclonal infections within TcI. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research.},
}
@article {pmid33325996,
year = {2020},
author = {Lannes, R and Cavaud, L and Lopez, P and Bapteste, E},
title = {Marine ultra-small prokaryotes likely affect the cycling of Carbon, Methane, Nitrogen and Sulfur.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaa261},
pmid = {33325996},
issn = {1759-6653},
abstract = {Recently, we uncovered the genetic components from six carbon fixation autotrophic pathways in cleaned ultra-small size fractions from marine samples (<0.22 micrometres) gathered worldwide by the Tara Oceans Expedition. This first finding suggested that prokaryotic nanoorganisms, phylogenetically distantly related to the known CPR and DPANN groups, could collectively impact carbon cycling and carbon fixation across the world's ocean. To extend our mining of the functional and taxonomic microbial dark matter from the ultra-small size fraction from the Tara Oceans Expedition, we investigated the distribution of 28 metabolic pathways associated with the cycling of carbon, methane, nitrogen and sulfur. For all of these pathways, we report the existence of novel metabolic homologs in the ultra-small size fraction of the oceanic microbiome, associated with nanoorganisms belonging to the CPR and DPANN lineages, but also of metabolic homologs exclusively found in marine host taxa belonging to other (still unassigned) microbial lineages. Therefore, we conclude that marine nanoorganisms contribute to a greater diversity of key biogeochemical cycles than currently appreciated. In particular, we suggest that oceanic nanoorganisms may be involved in a metabolic loop around Acetyl-CoA, have an underappreciated genetic potential to degrade methane, contribute to sustaining redox-reactions by producing Coenzyme F420, and affect sulfur cycling, notably as they harbour a complete suite of homologs of enzymes of the SOX system.},
}
@article {pmid33325795,
year = {2020},
author = {Chan, EWL and Chin, MY and Low, YH and Tan, HY and Ooi, YS and Chong, CW},
title = {The Antibacterial Agent Identified from Acidocella spp. in the Fluid of Nepenthes gracilis Against Multidrug-Resistant Klebsiella pneumoniae: A Functional Metagenomic Approach.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1089/mdr.2020.0311},
pmid = {33325795},
issn = {1931-8448},
abstract = {Aims: The fluid of Nepenthes gracilis harbors diverse bacterial taxa that could serve as a gene pool for the discovery of the new genre of antimicrobial agents against multidrug-resistant Klebsiella pneumoniae. The aim of this study was to explore the presence of antibacterial genes in the fluids of N. gracilis growing in the wild. Methods: Using functional metagenomic approach, fosmid clones were isolated and screened for antibacterial activity against three strains of K. pneumoniae. A clone that exhibited the most potent antibacterial activity was sent for sequencing to identify the genes responsible for the observed activity. The secondary metabolites secreted by the selected clone was sequentially extracted using hexane, chloroform, and ethyl acetate. The chemical profiles of a clone (C6) hexane extract were determined by gas chromatography/mass spectrometry (GC-MS). Results: Fosmid clone C6 from the fluid of pitcher plant that exhibited antibacterial activity against three strains of K. pneumoniae was isolated using functional metagenome approach. A majority of the open reading frames detected from C6 were affiliated with the largely understudied Acidocella genus. Among them, the gene that encodes for coproporphyrinogen III oxidase in the heme biosynthesis pathway could be involved in the observed antibacterial activity. Based on the GC-MS analysis, the identities of the putative bioactive compounds were 2,5-di-tert-butylphenol and 1-ethyl-2-methyl cyclododecane. Conclusions: The gene that encodes for coproporphyrinogen III oxidase in the heme biosynthesis pathway as well as the secondary metabolites, namely 2,5-di-tert-butylphenol and 1-ethyl-2-methyl cyclododecane could be the potential antibacterial molecules responsible for the antibacterial activity of C6.},
}
@article {pmid33323978,
year = {2020},
author = {Mirhakkak, MH and Schäuble, S and Klassert, TE and Brunke, S and Brandt, P and Loos, D and Uribe, RV and Senne de Oliveira Lino, F and Ni, Y and Vylkova, S and Slevogt, H and Hube, B and Weiss, GJ and Sommer, MOA and Panagiotou, G},
title = {Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {33323978},
issn = {1751-7370},
support = {210879364//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 210879364//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 210879364//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; NNF10CC1016517//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF10CC1016517//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 03Z22JN11//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
abstract = {Candida albicans is a leading cause of life-threatening hospital-acquired infections and can lead to Candidemia with sepsis-like symptoms and high mortality rates. We reconstructed a genome-scale C. albicans metabolic model to investigate bacterial-fungal metabolic interactions in the gut as determinants of fungal abundance. We optimized the predictive capacity of our model using wild type and mutant C. albicans growth data and used it for in silico metabolic interaction predictions. Our analysis of more than 900 paired fungal-bacterial metabolic models predicted key gut bacterial species modulating C. albicans colonization levels. Among the studied microbes, Alistipes putredinis was predicted to negatively affect C. albicans levels. We confirmed these findings by metagenomic sequencing of stool samples from 24 human subjects and by fungal growth experiments in bacterial spent media. Furthermore, our pairwise simulations guided us to specific metabolites with promoting or inhibitory effect to the fungus when exposed in defined media under carbon and nitrogen limitation. Our study demonstrates that in silico metabolic prediction can lead to the identification of gut microbiome features that can significantly affect potentially harmful levels of C. albicans.},
}
@article {pmid33323418,
year = {2020},
author = {López-Pérez, M and Haro-Moreno, JM and Iranzo, J and Rodriguez-Valera, F},
title = {Genomes of the &quot;Candidatus Actinomarinales&quot; Order: Highly Streamlined Marine Epipelagic Actinobacteria.},
journal = {mSystems},
volume = {5},
number = {6},
pages = {},
pmid = {33323418},
issn = {2379-5077},
abstract = {&quot;Candidatus Actinomarinales&quot; was defined as a subclass of exclusively marine Actinobacteria with small cells and genomes. We have collected all the available genomes in databases to assess the diversity included in this group and analyzed it by comparative genomics. We have found the equivalent of five genera and 18 genomospecies. They have genome reduction parameters equal to those of freshwater actinobacterial &quot;Candidatus Nanopelagicales&quot; or marine alphaproteobacterial Pelagibacterales Genome recruitment shows that they are found only in the photic zone and mainly in surface waters, with only one genus that is found preferentially at or below the deep chlorophyll maximum. &quot;Ca Actinomarinales&quot; show a highly conserved core genome (80% of the gene families conserved for the whole order) with a saturation of genomic diversity of the flexible genome at the genomospecies level. We found only a flexible genomic island preserved throughout the order; it is related to the sugar decoration of the envelope and uses several tRNAs as hot spots to increase its genomic diversity. Populations had a discrete level of sequence diversity similar to other marine microbes but drastically different from the much higher levels found for Pelagibacterales Genomic analysis suggests that they are all aerobic photoheterotrophs with one type 1 rhodopsin and a heliorhodopsin. Like other actinobacteria, they possess the F420 coenzyme biosynthesis pathway, and its lower reduction potential could provide access to an increased range of redox chemical transformations. Last, sequence analysis revealed the first &quot;Ca Actinomarinales&quot; phages, including a prophage, with metaviromic islands related to sialic acid cleavage.IMPORTANCE Microbiology is in a new age in which sequence databases are primary sources of information about many microbes. However, in-depth analysis of environmental genomes thus retrieved is essential to substantiate the new knowledge. Here, we study 182 genomes belonging to the only known exclusively marine pelagic group of the phylum Actinobacteria The aquatic branch of this phylum is largely known from environmental sequencing studies (single-amplified genomes [SAGs] and metagenome-assembled genomes [MAGs]), and we have collected and analyzed the available information present in databases about the &quot;Ca. Actinomarinales.&quot; They are among the most streamlined microbes to live in the epipelagic zone of the ocean, and their study is critical to obtain a proper view of the diversity of Actinobacteria and their role in aquatic ecosystems.},
}
@article {pmid33323122,
year = {2020},
author = {Shaiber, A and Willis, AD and Delmont, TO and Roux, S and Chen, LX and Schmid, AC and Yousef, M and Watson, AR and Lolans, K and Esen, ÖC and Lee, STM and Downey, N and Morrison, HG and Dewhirst, FE and Mark Welch, JL and Eren, AM},
title = {Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {292},
pmid = {33323122},
issn = {1474-760X},
support = {R35GM133420/NH/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE016937/DE/NIDCR NIH HHS/United States ; DE024468/DE/NIDCR NIH HHS/United States ; DE022586/DE/NIDCR NIH HHS/United States ; Frank R. Lillie Research Innovation Award//University of Chicago/ ; },
abstract = {INTRODUCTION: Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life.<br><br>RESULTS: Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment.<br><br>CONCLUSIONS: Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.},
}
@article {pmid33323004,
year = {2020},
author = {Van Hul, M and Le Roy, T and Prifti, E and Dao, MC and Paquot, A and Zucker, JD and Delzenne, NM and Muccioli, G and Clément, K and Cani, PD},
title = {From correlation to causality: the case of Subdoligranulum.},
journal = {Gut microbes},
volume = {12},
number = {1},
pages = {1-13},
doi = {10.1080/19490976.2020.1849998},
pmid = {33323004},
issn = {1949-0984},
abstract = {Gut microbes are considered as major factors contributing to human health. Nowadays, the vast majority of the data available in the literature are mostly exhibiting negative or positive correlations between specific bacteria and metabolic parameters. From these observations, putative detrimental or beneficial effects are then inferred. Akkermansia muciniphila is one of the unique examples for which the correlations with health benefits have been causally validated in vivo in rodents and humans. In this study, based on available metagenomic data in overweight/obese population and clinical variables that we obtained from two cohorts of individuals (n = 108) we identified several metagenomic species (MGS) strongly associated with A. muciniphila with one standing out: Subdoligranulum. By analyzing both qPCR and shotgun metagenomic data, we discovered that the abundance of Subdoligranulum was correlated positively with microbial richness and HDL-cholesterol levels and negatively correlated with fat mass, adipocyte diameter, insulin resistance, levels of leptin, insulin, CRP, and IL6 in humans. Therefore, to further explore whether these strong correlations could be translated into causation, we investigated the effects of the unique cultivated strain of Subdoligranulum (Subdoligranulum variabile DSM 15176 T) in obese and diabetic mice as a proof-of-concept. Strikingly, there were no significant difference in any of the hallmarks of obesity and diabetes measured (e.g., body weight gain, fat mass gain, glucose tolerance, liver weight, plasma lipids) at the end of the 8 weeks of treatment. Therefore, the absence of effect following the supplementation with S. variabile indicates that increasing the intestinal abundance of this bacterium is not translated into beneficial effects in mice. In conclusion, we demonstrated that despite the fact that numerous strong correlations exist between a given bacteria and health, proof-of-concept experiments are required to be further validated or not in vivo. Hence, an urgent need for causality studies is warranted to move from human observations to preclinical validations.},
}
@article {pmid33322999,
year = {2020},
author = {Zeng, Z and Luo, H and Huang, K and Xue, L and Liu, H and Li, X and Wang, L and Cen, H and Bi, W and Zhang, Y},
title = {Haemorrhagic cystitis following the administration of voriconazole in the treatment of central nervous system aspergillosis: a case report.},
journal = {The Journal of international medical research},
volume = {48},
number = {12},
pages = {300060520974924},
doi = {10.1177/0300060520974924},
pmid = {33322999},
issn = {1473-2300},
abstract = {Central nervous system aspergillosis (CNS-A) is a rare and fatal fungal infection. Voriconazole is the recommended treatment for CNS-A. The therapeutic effect of voriconazole is good, but its use is limited due to adverse reactions. This case report describes a 37-year-old male patient that had previously been diagnosed with acute lymphoblastic leukaemia. He had received immunosuppressive agents for 1 year following a haematopoietic bone marrow transplant. He presented with a 1-month history of left limb weakness as well as recurrent fever. Brain magnetic resonance imaging showed that he had multiple cerebral infarctions. Subsequently, he was diagnosed with CNS-A by metagenomic next-generation sequencing. Voriconazole was added to his treatment regimen, but it resulted in severe haemorrhagic cystitis and possibly bladder rupture. The dose of voriconazole was adjusted and reparative bladder surgery was undertaken immediately. Eventually, the patient was successfully treated with voriconazole and there was no recurrence of symptoms after 1 year of follow-up. Haemorrhagic cystitis is a rare adverse drug reaction associated with voriconazole use. Based on the experience with this current case, physicians should be aware of urinary tract complications with voriconazole including haemorrhagic cystitis.},
}
@article {pmid33322135,
year = {2020},
author = {Fernandez-Cassi, X and Martínez-Puchol, S and Silva-Sales, M and Cornejo, T and Bartolome, R and Bofill-Mas, S and Girones, R},
title = {Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach.},
journal = {Viruses},
volume = {12},
number = {12},
pages = {},
pmid = {33322135},
issn = {1999-4915},
abstract = {Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new opportunities for viral pathogen detection and discovery. Viral metagenomics in routine clinical settings has the potential to identify unexpected or novel variants of viral pathogens that cause gastroenteritis. In this study, 124 samples from acute gastroenteritis patients from 2012-2014 previously tested negative for common gastroenteritis pathogens were pooled by age and analyzed by next generation sequencing (NGS) to elucidate unidentified viral infections. The most abundant sequences detected potentially associated to acute gastroenteritis were from Astroviridae and Caliciviridae families, with the detection of norovirus GIV and sapoviruses. Lower number of contigs associated to rotaviruses were detected. As expected, other viruses that may be associated to gastroenteritis but also produce persistent infections in the gut were identified including several Picornaviridae members (EV, parechoviruses, cardioviruses) and adenoviruses. According to the sequencing data, astroviruses, sapoviruses and NoV GIV should be added to the list of viral pathogens screened in routine clinical analysis.},
}
@article {pmid33322131,
year = {2020},
author = {Patil, HJ and Gatica, J and Zolti, A and Benet-Perelberg, A and Naor, A and Dror, B and Al Ashhab, A and Marman, S and Hasan, NA and Colwell, RR and Sher, D and Minz, D and Cytryn, E},
title = {Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33322131},
issn = {2076-2607},
abstract = {Excessive use of antimicrobials in aquaculture is concerning, given possible environmental ramifications and the potential contribution to the spread of antimicrobial resistance (AR). In this study, we explored seasonal abundance of antimicrobial resistance genes and bacterial community composition in the water column of an intensive aquaculture pond stocked with Silver Carp (Hypophthalmichthys molitrix) prophylactically treated with sulfamethoprim (25% sulfadiazine; 5% trimethoprim), relative to an adjacent unstocked reservoir. Bacterial community composition was monitored using high-throughput sequencing of 16S rRNA gene amplicons in eight sampling profiles to determine seasonal dynamics, representing principal stages in the fish fattening cycle. In tandem, qPCR was applied to assess relative abundance of selected antimicrobial resistance genes (sul1, sul2, dfrA1, tetA and blaTEM) and class-1 integrons (int1). Concomitantly, resistomes were extrapolated from shotgun metagenomes in representative profiles. Analyses revealed increased relative abundance of sulfonamide and tetracycline resistance genes in fishpond-03, relative to pre-stocking and reservoir levels, whereas no significant differences were observed for genes encoding resistance to antimicrobials that were not used in the fishpond-03. Seasons strongly dictated bacterial community composition, with high abundance of cyanobacteria in summer and increased relative abundance of Flavobacterium in the winter. Our results indicate that prophylactic use of sulfonamides in intensive aquaculture ponds facilitates resistance suggesting that prophylactic use of these antimicrobials in aquaculture should be restricted.},
}
@article {pmid33322070,
year = {2020},
author = {Martí-Carreras, J and Gener, AR and Miller, SD and Brito, AF and Camacho, CE and Connor, R and Deboutte, W and Glickman, C and Kristensen, DM and Meyer, WK and Modha, S and Norris, AL and Saha, S and Belford, AK and Biederstedt, E and Brister, JR and Buchmann, JP and Cooley, NP and Edwards, RA and Javkar, K and Muchow, M and Muralidharan, HS and Pepe-Ranney, C and Shah, N and Shakya, M and Tisza, MJ and Tully, BJ and Vanmechelen, B and Virta, VC and Weissman, JL and Zalunin, V and Efremov, A and Busby, B},
title = {NCBI's Virus Discovery Codeathon: Building &quot;FIVE&quot; -The Federated Index of Viral Experiments API Index.},
journal = {Viruses},
volume = {12},
number = {12},
pages = {},
pmid = {33322070},
issn = {1999-4915},
support = {T15 LM007059/LM/NLM NIH HHS/United States ; RC2 DK116713/DK/NIDDK NIH HHS/United States ; },
abstract = {Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus-host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.},
}
@article {pmid33321431,
year = {2020},
author = {Misery, B and Legendre, P and Rue, O and Bouchart, V and Guichard, H and Laplace, JM and Cretenet, M},
title = {Diversity and dynamics of bacterial and fungal communities in cider for distillation.},
journal = {International journal of food microbiology},
volume = {339},
number = {},
pages = {108987},
doi = {10.1016/j.ijfoodmicro.2020.108987},
pmid = {33321431},
issn = {1879-3460},
abstract = {Bacterial and fungal population dynamics in cider for distillation have so far been explored by culture-dependant methods. Cider for distillation can be produced by the spontaneous fermentation of apples that do not undergo any intervention during the process. In this study, cider microbiomes extracted from six tanks containing ciders for distillation from four producers in Normandy were characterized at three main stages of the fermentation process: fermentation Initiation (I), end of the alcoholic Fermentation (F) and end of the Maturation period (M). Cider samples were subjected to Illumina MiSeq sequencing (rRNA 16S V1-V3 and ITS1 region targeting) to determine bacterial and fungal communities. Yeasts (YGC), Zymomonas (mZPP) and lactic acid bacteria selective media (mMRS, mMLO, mPSM) were also used to collect 807 isolates. Alcoholic levels, glycerol, sugar content (glucose, fructose and sucrose), pH, total and volatile acidity, nitrogen, malic and lactic acid contents were determined at all sampling points. Alpha diversity indexes show significant differences (p < 0.05) in microbial populations between I, F and M. Fungal communities were characterized by microorganisms from the environment and phytopathogens at I followed by the association of yearsts with alcoholic fermentation like Saccharomyces and non-Saccharomyces yeasts (Hanseniaspora, Candida). A maturation period for cider leads to an increase of the Dekkera/Brettanomyces population, which is responsible for off-flavors in cider for all producers. Among bacterial communities, the genera community associated to malolactic fermentation (Lactobacillus sp., Leuconostoc sp., Oenococcus sp.) was the most abundant at F and M. Acetic acid bacteria such as Acetobacter sp., Komagataeibacter sp. and Gluconobacter sp. were also detected during the process. Significant differences (p < 0.05) were found in fungal and bacterial populations between the four producers and during the fermentation process. The development of microorganisms associated with cider spoilage such as Zymomonas mobilis, Lactobacillus collinoides or Brettanomyces/Dekkera sp. was anticipated by a metagenomic approach. The monitoring of microbial diversity via high throughput sequencing combined with physical-chemical analysis is an interesting approach to improve the fermentation performance of cider for distillation and therefore, the quality of Calvados.},
}
@article {pmid33321144,
year = {2020},
author = {Yu, G and Wang, X and Zhu, P and Shen, Y and Zhao, W and Zhou, L},
title = {Comparison of the efficacy of metagenomic next-generation sequencing and Xpert MTB/RIF in the diagnosis of tuberculous meningitis.},
journal = {Journal of microbiological methods},
volume = {180},
number = {},
pages = {106124},
doi = {10.1016/j.mimet.2020.106124},
pmid = {33321144},
issn = {1872-8359},
abstract = {Metagenomic next-generation sequencing (mNGS) is an emerging sequence-based method that detects genomic information of pathogenic microorganisms from a wide range of clinical specimens. The mNGS has moderate sensitivity and very high specificity for tuberculous meningitis, and the validity of mNGS was higher than that of Xpert MTB/RIF.},
}
@article {pmid33319812,
year = {2020},
author = {Pust, MM and Wiehlmann, L and Davenport, C and Rudolf, I and Dittrich, AM and Tümmler, B},
title = {The human respiratory tract microbial community structures in healthy and cystic fibrosis infants.},
journal = {NPJ biofilms and microbiomes},
volume = {6},
number = {1},
pages = {61},
pmid = {33319812},
issn = {2055-5008},
support = {158989968//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {The metagenome development of the human respiratory tract was investigated by shotgun metagenome metagenomic sequencing of cough swabs from healthy children and children with cystic fibrosis (CF) between 3 weeks and 6 years of age. A healthy microbial community signature was associated with increased absolute abundances in terms of bacterial-human cell ratios of core and rare species across all age groups, with a higher diversity of rare species and a tightly interconnected species co-occurrence network, in which individual members were found in close proximity to each other and negative correlations were absent. Even without typical CF pathogens, the CF infant co-occurrence network was found to be less stable and prone to fragmentation due to fewer connections between species, a higher number of bridging species and the presence of negative species correlations. Detection of low-abundant DNA of the CF hallmark pathogen Pseudomonas aeruginosa was neither disease- nor age-associated in our cohort. Healthy and CF children come into contact with P. aeruginosa on a regular basis and from early on.},
}
@article {pmid33319778,
year = {2020},
author = {Wylensek, D and Hitch, TCA and Riedel, T and Afrizal, A and Kumar, N and Wortmann, E and Liu, T and Devendran, S and Lesker, TR and Hernández, SB and Heine, V and Buhl, EM and M D'Agostino, P and Cumbo, F and Fischöder, T and Wyschkon, M and Looft, T and Parreira, VR and Abt, B and Doden, HL and Ly, L and Alves, JMP and Reichlin, M and Flisikowski, K and Suarez, LN and Neumann, AP and Suen, G and de Wouters, T and Rohn, S and Lagkouvardos, I and Allen-Vercoe, E and Spröer, C and Bunk, B and Taverne-Thiele, AJ and Giesbers, M and Wells, JM and Neuhaus, K and Schnieke, A and Cava, F and Segata, N and Elling, L and Strowig, T and Ridlon, JM and Gulder, TAM and Overmann, J and Clavel, T},
title = {A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {6389},
pmid = {33319778},
issn = {2041-1723},
abstract = {Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called 'Pig intestinal bacterial collection' (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.},
}
@article {pmid33319480,
year = {2020},
author = {Mushinski, RM and Payne, ZC and Raff, JD and Craig, ME and Pusede, SE and Rusch, DB and White, JR and Phillips, RP},
title = {Nitrogen cycling microbiomes are structured by plant mycorrhizal associations with consequences for nitrogen oxide fluxes in forests.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.15439},
pmid = {33319480},
issn = {1365-2486},
support = {2013-67011-21095//US Department of Agriculture/ ; DE-AC02-05CH11231//US Department of Energy Joint Genome Institute/ ; DE-SC0014443//US Department of Energy/ ; 2018-08037//US Department of Agriculture National Institute of Food and Agriculture/ ; AGS-1352375//NSF/ ; DE-AC05-00OR22725//Oak Ridge National Laboratory/ ; },
abstract = {Volatile nitrogen oxides (N2 O, NO, NO2 , HONO, …) can negatively impact climate, air quality, and human health. Using soils collected from temperate forests across the eastern United States, we show microbial communities involved in nitrogen (N) cycling are structured, in large part, by the composition of overstory trees, leading to predictable N-cycling syndromes, with consequences for emissions of volatile nitrogen oxides to air. Trees associating with arbuscular mycorrhizal (AM) fungi promote soil microbial communities with higher N-cycle potential and activity, relative to microbial communities in soils dominated by trees associating with ectomycorrhizal (ECM) fungi. Metagenomic analysis and gene expression studies reveal a 5 and 3.5 times greater estimated N-cycle gene and transcript copy numbers, respectively, in AM relative to ECM soil. Furthermore, we observe a 60% linear decrease in volatile reactive nitrogen gas flux (NOy ≡ NO, NO2 , HONO) as ECM tree abundance increases. Compared to oxic conditions, gas flux potential of N2 O and NO increase significantly under anoxic conditions for AM soil (30- and 120-fold increase), but not ECM soil-likely owing to small concentrations of available substrate (NO 3 -) in ECM soil. Linear mixed effects modeling shows that ECM tree abundance, microbial process rates, and geographic location are primarily responsible for variation in peak potential NOy flux. Given that nearly all tree species associate with either AM or ECM fungi, our results indicate that the consequences of tree species shifts associated with global change may have predictable consequences for soil N cycling.},
}
@article {pmid33318859,
year = {2020},
author = {Charre, C and Ginevra, C and Sabatier, M and Regue, H and Destras, G and Brun, S and Burfin, G and Scholtes, C and Morfin, F and Valette, M and Lina, B and Bal, A and Josset, L},
title = {Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation.},
journal = {Virus evolution},
volume = {6},
number = {2},
pages = {veaa075},
doi = {10.1093/ve/veaa075},
pmid = {33318859},
issn = {2057-1577},
abstract = {Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next-Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty-four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialised kits including a hybridisation capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP), and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (>99%) for high viral loads samples (n = 8), with mNGS and RVOP producing the most complete genomes. For mid viral loads (Ct 20-25), amplicon-based enrichment methods led to genome coverage >99 per cent for all samples while 1/8 sample sequenced with RVOP and 2/8 samples sequenced with mNGS had a genome coverage below 99 per cent. For low viral loads (Ct ≥25), amplicon-based enrichment methods were the most sensitive techniques. All methods were highly concordant in terms of identity in complete consensus sequence. Just one mismatch in three samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. Importantly, all methods correctly identified a newly observed 34nt-deletion in ORF6 but required specific bioinformatic validation for RVOP. Finally, as a major warning for targeted techniques, a loss of coverage in any given region of the genome should alert to a potential rearrangement or a SNP in primer-annealing or probe-hybridizing regions and would require further validation using unbiased metagenomic sequencing.},
}
@article {pmid33318237,
year = {2020},
author = {Hosgood, HD and Cai, Q and Hua, X and Long, J and Shi, J and Wan, Y and Yang, Y and Abnet, C and Bassig, BA and Hu, W and Ji, BT and Klugman, M and Xiang, Y and Gao, YT and Wong, JY and Zheng, W and Rothman, N and Shu, XO and Lan, Q},
title = {Variation in oral microbiome is associated with future risk of lung cancer among never-smokers.},
journal = {Thorax},
volume = {},
number = {},
pages = {},
doi = {10.1136/thoraxjnl-2020-215542},
pmid = {33318237},
issn = {1468-3296},
abstract = {OBJECTIVE: To prospectively investigate whether diversity in oral microbiota is associated with risk of lung cancer among never-smokers.<br><br>DESIGN AND SETTING: A nested case-control study within two prospective cohort studies, the Shanghai Women's Health Study (n=74 941) and the Shanghai Men's Health Study (n=61 480).<br><br>PARTICIPANTS: Lifetime never-smokers who had no cancer at baseline. Cases were subjects who were diagnosed with incident lung cancer (n=114) and were matched 1:1 with controls on sex, age (≤2 years), date (≤30 days) and time (morning/afternoon) of sample collection, antibiotic use during the week before sample collection (yes/no) and menopausal status (for women).<br><br>MAIN OUTCOMES AND MEASURES: Metagenomic shotgun sequencing was used to measure the community structure and abundance of the oral microbiome in pre-diagnostic oral rinse samples of each case and control. Multivariable logistic regression models were used to estimate the association of lung cancer risk with alpha diversity metrics and relative abundance of taxa. The Microbiome Regression-Based Kernel Association Test (MiRKAT) evaluated the association between risk and the microbiome beta diversity.<br><br>RESULTS: Subjects with lower microbiota alpha diversity had an increased risk of lung cancer compared with those with higher microbial alpha diversity (Shannon: ptrend=0.05; Simpson: ptrend=0.04; Observed Species: ptrend=0.64). No case-control differences were apparent for beta diversity (pMiRKAT=0.30). After accounting for multiple comparisons, a greater abundance of Spirochaetia (ORlow 1.00 (reference), ORmedium 0.61 (95% CI 0.32 to 1.18), ORhigh 0.42 (95% CI 0.21 to 0.85)) and Bacteroidetes (ORlow 1.00 (reference), ORmedium 0.66 (95% CI 0.35 to 1.25), ORhigh 0.31 (95% CI 0.15 to 0.64)) was associated with a decreased risk of lung cancer, while a greater abundance of the Bacilli class (ORlow 1.00 (reference), ORmedium 1.49 (95% CI 0.73 to 3.08), ORhigh 2.40 (95% CI 1.18 to 4.87)) and Lactobacillales order (ORlow 1.00 (reference), ORmedium 2.15 (95% CI 1.03 to 4.47), ORhigh 3.26 (95% CI 1.58 to 6.70)) was associated with an increased risk of lung cancer.<br><br>CONCLUSIONS: Our prospective study of never-smokers suggests that lower alpha diversity was associated with a greater risk of lung cancer and the abundance of certain specific taxa was associated with altered risk, providing further insight into the aetiology of lung cancer in the absence of active tobacco smoking.},
}
@article {pmid33318221,
year = {2020},
author = {Gao, Q and Wang, G and Xue, K and Yang, Y and Xie, J and Yu, H and Bai, S and Liu, F and He, Z and Ning, D and Hobbie, SE and Reich, PB and Zhou, J},
title = {Stimulation of soil respiration by elevated CO2 is enhanced under nitrogen limitation in a decade-long grassland study.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {52},
pages = {33317-33324},
doi = {10.1073/pnas.2002780117},
pmid = {33318221},
issn = {1091-6490},
abstract = {Whether and how CO2 and nitrogen (N) availability interact to influence carbon (C) cycling processes such as soil respiration remains a question of considerable uncertainty in projecting future C-climate feedbacks, which are strongly influenced by multiple global change drivers, including elevated atmospheric CO2 concentrations (eCO2) and increased N deposition. However, because decades of research on the responses of ecosystems to eCO2 and N enrichment have been done largely independently, their interactive effects on soil respiratory CO2 efflux remain unresolved. Here, we show that in a multifactor free-air CO2 enrichment experiment, BioCON (Biodiversity, CO2, and N deposition) in Minnesota, the positive response of soil respiration to eCO2 gradually strengthened at ambient (low) N supply but not enriched (high) N supply for the 12-y experimental period from 1998 to 2009. In contrast to earlier years, eCO2 stimulated soil respiration twice as much at low than at high N supply from 2006 to 2009. In parallel, microbial C degradation genes were significantly boosted by eCO2 at low but not high N supply. Incorporating those functional genes into a coupled C-N ecosystem model reduced model parameter uncertainty and improved the projections of the effects of different CO2 and N levels on soil respiration. If our observed results generalize to other ecosystems, they imply widely positive effects of eCO2 on soil respiration even in infertile systems.},
}
@article {pmid33317254,
year = {2020},
author = {Lee, NY and Shin, MJ and Youn, GS and Yoon, SJ and Choi, YR and Kim, HS and Gupta, H and Han, SH and Kim, BK and Lee, DY and Park, TS and Sung, H and Kim, BY and Suk, KT},
title = {Lactobacillus attenuates progression of non-alcoholic fatty liver disease by lowering cholesterol and steatosis.},
journal = {Clinical and molecular hepatology},
volume = {},
number = {},
pages = {},
doi = {10.3350/cmh.2020.0125},
pmid = {33317254},
issn = {2287-285X},
abstract = {Background/Aims: Non-alcoholic fatty liver disease (NAFLD) is closely related to gut-microbiome. There is a paucity of research on which strains of gut microbiota affecting the progression of NAFLD. This study explored NAFLD-associated microbiome in humans and the role of Lactobacillus in the progression of NAFLD in mice.<br><br>Methods: The gut microbiome was analyzed via NGS in healthy people (n=37) and NAFLD patients with elevated liver enzymes (n=57). Six weeks male C57BL/6J mice were separated into 6-group (n=10/group; normal, Western, and four Western diet+ strains [109 43 CFU/g for 8-week; L. acidophilus, L. fermentum, L. paracasei, and L. plantarum]). Liver/body weight ratio, liver pathology, serum analysis, and metagenomics in the mice were examined.<br><br>Results: Compared with healthy subjects (1.6±4.3), NAFLD patients showed an elevated Firmicutes/Bacteroidetes ratio (25.0±29.0) and a reduced composition of Akkermansia and L. murinus (p<0.05). In the animal experiment, L. acidophilus group was associated with a significant reduction in liver/body weight ratio (5.5±0.4) compared with the Western group (6.2±0.6) (p <0.05). L. acidophilus (41.0±8.6), L. fermentum (44.3±12.6), and L. plantarum (39.0±7.6) groups showed decreased cholesterol levels compared with the Western group (85.7±8.6) (p <0.05). In comparison of steatosis, L. acidophilus (1.9±0.6), L. plantarum (2.4±0.7), and L. paracasei (2.0±0.9) groups showed significant improvement of steatosis, compared with the Western group (2.6±0.5)(p <0.05).<br><br>Conclusion: Ingestion of Lactobacillus, such as L. acidophilus, L. fermentum, and L. plantarum ameliorates the progression of nonalcoholic steatosis by lowering cholesterol. The use of Lactobacillus can be considered as a useful strategy for the treatment of NAFLD.},
}
@article {pmid33317082,
year = {2020},
author = {Afridi, OK and Ali, J and Chang, JH},
title = {Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli.},
journal = {Animals : an open access journal from MDPI},
volume = {10},
number = {12},
pages = {},
pmid = {33317082},
issn = {2076-2615},
support = {grand No. NRF-2019R1A2C4069796//Basic Science Research Program of the National Research Foundation of Korea and the Ministry of Science and ICT/ ; },
abstract = {The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) Escherichia coli (E. coli). Fecal samples (n = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR E. coli. Upon initial screening, thirteen (13) MDR E. coli isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were iroN, iutA, iss, and iucA. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as E. coli, Salmonella enterica, Klebsiella pneumoniae, and Shigella flexneri belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR E. coli of Khyber Pakhtunkhwa for the first time using NGS.},
}
@article {pmid33317070,
year = {2020},
author = {Bergsten, E and Mestivier, D and Sobhani, I},
title = {The Limits and Avoidance of Biases in Metagenomic Analyses of Human Fecal Microbiota.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33317070},
issn = {2076-2607},
abstract = {An increasing body of evidence highlights the role of fecal microbiota in various human diseases. However, more than two-thirds of fecal bacteria cannot be cultivated by routine laboratory techniques. Thus, physicians and scientists use DNA sequencing and statistical tools to identify associations between bacterial subgroup abundances and disease. However, discrepancies between studies weaken these results. In the present study, we focus on biases that might account for these discrepancies. First, three different DNA extraction methods (G'NOME, QIAGEN, and PROMEGA) were compared with regard to their efficiency, i.e., the quality and quantity of DNA recovered from feces of 10 healthy volunteers. Then, the impact of the DNA extraction method on the bacteria identification and quantification was evaluated using our published cohort of sample subjected to both 16S rRNA sequencing and whole metagenome sequencing (WMS). WMS taxonomical assignation employed the universal marker genes profiler mOTU-v2, which is considered the gold standard. The three standard pipelines for 16S RNA analysis (MALT and MEGAN6, QIIME1, and DADA2) were applied for comparison. Taken together, our results indicate that the G'NOME-based method was optimal in terms of quantity and quality of DNA extracts. 16S rRNA sequence-based identification of abundant bacteria genera showed acceptable congruence with WMS sequencing, with the DADA2 pipeline yielding the highest congruent levels. However, for low abundance genera (<0.5% of the total abundance) two pipelines and/or validation by quantitative polymerase chain reaction (qPCR) or WMS are required. Hence, 16S rRNA sequencing for bacteria identification and quantification in clinical and translational studies should be limited to diagnostic purposes in well-characterized and abundant genera. Additional techniques are warranted for low abundant genera, such as WMS, qPCR, or the use of two bio-informatics pipelines.},
}
@article {pmid33316921,
year = {2020},
author = {Tonkovic, P and Kalajdziski, S and Zdravevski, E and Lameski, P and Corizzo, R and Pires, IM and Garcia, NM and Loncar-Turukalo, T and Trajkovik, V},
title = {Literature on Applied Machine Learning in Metagenomic Classification: A Scoping Review.},
journal = {Biology},
volume = {9},
number = {12},
pages = {},
pmid = {33316921},
issn = {2079-7737},
support = {UIDB/50008/2020//FCT/MEC/ ; CA16226//European Commission/ ; },
abstract = {Applied machine learning in bioinformatics is growing as computer science slowly invades all research spheres. With the arrival of modern next-generation DNA sequencing algorithms, metagenomics is becoming an increasingly interesting research field as it finds countless practical applications exploiting the vast amounts of generated data. This study aims to scope the scientific literature in the field of metagenomic classification in the time interval 2008-2019 and provide an evolutionary timeline of data processing and machine learning in this field. This study follows the scoping review methodology and PRISMA guidelines to identify and process the available literature. Natural Language Processing (NLP) is deployed to ensure efficient and exhaustive search of the literary corpus of three large digital libraries: IEEE, PubMed, and Springer. The search is based on keywords and properties looked up using the digital libraries' search engines. The scoping review results reveal an increasing number of research papers related to metagenomic classification over the past decade. The research is mainly focused on metagenomic classifiers, identifying scope specific metrics for model evaluation, data set sanitization, and dimensionality reduction. Out of all of these subproblems, data preprocessing is the least researched with considerable potential for improvement.},
}
@article {pmid33316516,
year = {2020},
author = {Tian, L and Wang, L},
title = {Multi-omics analysis reveals structure and function of biofilm microbial communities in a pre-denitrification biofilter.},
journal = {The Science of the total environment},
volume = {757},
number = {},
pages = {143908},
doi = {10.1016/j.scitotenv.2020.143908},
pmid = {33316516},
issn = {1879-1026},
abstract = {The highly complex microbial communities in biofilm play crucial roles in the pollutant removal performance of wastewater treatment plants (WWTPs). In the present study, using multi-omics analysis, we studied microbial structure, key enzymes, functional traits, and key metabolic pathways of pre-denitrification biofilter in an urban WWTP in China. The analysis results of metagenomic and metaproteomic showed that Betaproteobacteria and Flavobacteriia were dominant in biofilms. The integrated metagenomic and metaproteomic data showed that the expression of nitrogen metabolism genes was high, and the high proportion of denitrification module indicating that denitrification was the main nitrogen removal pathway. The most abundant denitrifying bacterial genera were: Dechloromonas, Acidovorax, Bosea, Polaromonas, and Chryseobacterium. And microorganisms with denitrification potential may not be able to denitrify in the actual operation of the filter. The integrated analysis of metaproteomic and metabolomic showed that there was a correlation between biofilm microorganisms and metabolites. Metabolomic analysis indicated that metabolic profiles of biofilms varied with layer height. This study provides the first detailed microbial communities and metabolic profiles in a full-scale pre-denitrification biofilter and clarifies the mechanism of denitrification.},
}
@article {pmid33316338,
year = {2020},
author = {Pabbathi, NPP and Velidandi, A and Gandam, PK and Koringa, P and Parcha, SR and Baadhe, RR},
title = {Novel buffalo rumen metagenome derived acidic cellulase Cel-3.1 cloning, characterization, and its application in saccharifying rice straw and corncob biomass.},
journal = {International journal of biological macromolecules},
volume = {170},
number = {},
pages = {239},
doi = {10.1016/j.ijbiomac.2020.12.041},
pmid = {33316338},
issn = {1879-0003},
abstract = {Lignocellulosic biomass (LCB) is a prominent option for second-generation biofuels production. Cellulase hydrolyses cellulose, a component of LCB by attacking the β-1,4-glycosidic bonds, thus liberating mono, di, and oligosaccharides, which subsequently, can be converted to biofuel. In this study, a novel cellulase (Cel-3.1) of 1593 bp which encodes a 530 amino acid protein was identified from buffalo rumen metagenomic fosmid library, and functional expression was achieved through transformation into Escherichia coli. The molecular weight was estimated as 58 kDa on SDS-PAGE. Cel-3.1 belongs to glycosyl hydrolase family-5 (GH-5) and is predicted to have 14 α-helices and 15 β-strands. The optimal temperature and pH for Cel-3.1 were experimentally determined as 5.0 and 50 °C respectively. The synergistic effect of Ca2+ with K+ ions improved Cel-3.1 activity significantly (25%) and 1% Polyethylene Glycol (PEG-400), 1% β-mercaptoethanol enhanced the relative activity Cel-3.1 by 31.68%, 12.03% respectively. Further, the enzymatic (Cel-3.1) hydrolysis of pretreated rice straw and corncob released 13.41 ± 0.26 mg/mL and 15.04 ± 0.08 mg/mL reducing sugars respectively. High Performance Liquid Chromatography (HPLC), Scanning Electron Microscope (SEM), and Fourier Transformation Infrared spectroscopy (FTIR) analysis revealed the capability of Cel-3.1 for the breakdown and hydrolysis of both rice straw and corncob to generate various fermentable sugars.},
}
@article {pmid33316292,
year = {2020},
author = {Romanis, CS and Pearson, LA and Neilan, BA},
title = {Cyanobacterial blooms in wastewater treatment facilities: Significance and emerging monitoring strategies.},
journal = {Journal of microbiological methods},
volume = {180},
number = {},
pages = {106123},
doi = {10.1016/j.mimet.2020.106123},
pmid = {33316292},
issn = {1872-8359},
abstract = {Municipal wastewater treatment facilities (WWTFs) are prone to the proliferation of cyanobacterial species which thrive in stable, nutrient-rich environments. Dense cyanobacterial blooms frequently disrupt treatment processes and the supply of recycled water due to their production of extracellular polymeric substances, which hinder microfiltration, and toxins, which pose a health risk to end-users. A variety of methods are employed by water utilities for the identification and monitoring of cyanobacteria and their toxins in WWTFs, including microscopy, flow cytometry, ELISA, chemoanalytical methods, and more recently, molecular methods. Here we review the literature on the occurrence and significance of cyanobacterial blooms in WWTFs and discuss the pros and cons of the various strategies for monitoring these potentially hazardous events. Particular focus is directed towards next-generation metagenomic sequencing technologies for the development of site-specific cyanobacterial bloom management strategies. Long-term multi-omic observations will enable the identification of indicator species and the development of site-specific bloom dynamics models for the mitigation and management of cyanobacterial blooms in WWTFs. While emerging metagenomic tools could potentially provide deep insight into the diversity and flux of problematic cyanobacterial species in these systems, they should be considered a complement to, rather than a replacement of, quantitative chemoanalytical approaches.},
}
@article {pmid33316049,
year = {2020},
author = {Rissanen, AJ and Saarela, T and Jäntti, H and Buck, M and Peura, S and Aalto, SL and Ojala, A and Pumpanen, J and Tiirola, M and Elvert, M and Nykänen, H},
title = {Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaa252},
pmid = {33316049},
issn = {1574-6941},
abstract = {The vertical structuring of methanotrophic communities and its genetic controllers remain understudied in the water columns of oxygen-stratified lakes. Therefore, we used 16S rRNA gene sequencing to study the vertical stratification patterns of methanotrophs in two boreal lakes, Lake Kuivajärvi and Lake Lovojärvi. Furthermore, metagenomic analyses were done to assess the genomic characteristics of methanotrophs in Lovojärvi and a previously studied Lake Alinen Mustajärvi. The methanotroph communities were vertically structured along the oxygen gradient. Alphaproteobacterial methanotrophs preferred oxic water layers, while Methylococcales methanotrophs, consisting of putative novel genera and species, thrived especially at and below the oxic-anoxic interface and showed distinct depth variation patterns, which were not completely predictable by their taxonomic classification. Instead, genomic differences among Methylococcales methanotrophs explained their variable vertical depth patterns. Genes in COG categories L (Replication, recombination and repair) and S (Function unknown) were relatively high in metagenome-assembled-genomes representing Methylococcales thriving clearly below the oxic-anoxic interface, suggesting genetic adaptations for increased stress tolerance enabling living in the hypoxic/anoxic conditions. In contrast, genes in COG category N (Cell motility) were relatively high in metagenome-assembled-genomes of Methylococcales thriving at the oxic-anoxic interface, which suggests genetic adaptations for increased motility at the vertically fluctuating oxic-anoxic interface.},
}
@article {pmid33315571,
year = {2020},
author = {Liu, F and Miao, Y and Liu, Y and Hou, T},
title = {RNN-VirSeeker: a deep learning method for identification of short viral sequences from metagenomes.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBB.2020.3044575},
pmid = {33315571},
issn = {1557-9964},
abstract = {Viruses are the most abundant biological entities on earth, and play vital roles in many aspects of microbial communities. As major human pathogens, viruses have caused huge mortality and morbidity to human society in history. Metagenomic sequencing methods could capture all microorganisms from microbiota, with sequences of viruses mixed with these of other species. Therefore, it is necessary to identify viral sequences from metagenomes. However, existing methods perform poorly on identifying short viral sequences. To solve this problem, a deep learning based method, RNN-VirSeeker, is proposed in this paper. RNN-VirSeeker was trained by sequences of 500bp sampled from known Virus and Host RefSeq genomes. Experimental results on the testing set have shown that RNN-VirSeeker exhibited AUROC of 0.9175, recall of 0.8640 and precision of 0.9211 for sequences of 500bp, and outperformed three widely used methods, VirSorter, VirFinder, and DeepVirFinder, on identifying short viral sequences. RNN-VirSeeker was also used to identify viral sequences from a CAMI dataset and a human gut metagenome. Compared with DeepVirFinder, RNN-VirSeeker identified more viral sequences from these metagenomes and achieved greater values of AUPRC and AUROC. RNN-VirSeeker is freely available at https://github.com/crazyinter/RNN-VirSeeker.},
}
@article {pmid33314800,
year = {2020},
author = {Artacho, A and Isaac, S and Nayak, R and Flor-Duro, A and Alexander, M and Koo, I and Manasson, J and Smith, PB and Rosenthal, P and Homsi, Y and Gulko, P and Pons, J and Puchades-Carrasco, L and Izmirly, P and Patterson, A and Abramson, SB and Pineda-Lucena, A and Turnbaugh, PJ and Ubeda, C and Scher, JU},
title = {The Pre-treatment Gut Microbiome is Associated with Lack of Response to Methotrexate in New Onset Rheumatoid Arthritis.},
journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.41622},
pmid = {33314800},
issn = {2326-5205},
abstract = {OBJECTIVES: Although oral methotrexate (MTX) remains the anchor drug for RA, up to 50% of patients do not achieve a clinically adequate outcome. Concomitantly, there is a lack of prognostic tools for treatment response prior to drug initiation. Here we study whether inter-individual differences in the human gut microbiome can aid in the prediction of MTX efficacy in new-onset RA (NORA).<br><br>METHODS: 16S rRNA gene and shotgun metagenomic sequencing were performed on the baseline gut microbiomes of drug-naïve, NORA patients (n=26). Results were validated in an additional independent cohort (n=21). To gain insight into potential microbial mechanisms, ex vivo experiments coupled with metabolomics analysis evaluated the association between microbiome-driven MTX depletion and clinical response.<br><br>RESULTS: Our analysis revealed significant associations between the abundance of gut bacterial taxa and their genes with future clinical response, including orthologs related to purine and methotrexate metabolism. Machine learning techniques were applied to the metagenomic data, resulting in a microbiome-based model that predicts lack of response to MTX in an independent group of patients. Finally, MTX levels remaining after ex vivo incubation with distal gut samples from pre-treatment RA patients significantly correlated with the magnitude of future clinical response, suggesting a possible direct effect of the gut microbiome on MTX metabolism and treatment outcomes.<br><br>CONCLUSIONS: Together, these results provide the first step towards predicting lack of response to oral MTX in NORA patients and support the value of the gut microbiome as a possible prognostic tool and as a potential target in RA therapeutics.},
}
@article {pmid33314183,
year = {2020},
author = {Chumpitazi, BP and Hoffman, KL and Smith, DP and McMeans, AR and Musaad, S and Versalovic, J and Petrosino, JF and Shulman, RJ},
title = {Fructan-sensitive children with irritable bowel syndrome have distinct gut microbiome signatures.},
journal = {Alimentary pharmacology &amp; therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.16204},
pmid = {33314183},
issn = {1365-2036},
support = {K23 DK101688/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R03 DK117219/DK/NIDDK NIH HHS/United States ; UH3 DK083990/DK/NIDDK NIH HHS/United States ; 6250-51000-043//United States Department of Agriculture/Agriculture Research Service/ ; },
abstract = {BACKGROUND: Dietary fructans may worsen gastrointestinal symptoms in children with irritable bowel syndrome (IBS).<br><br>AIM: To determine whether gut microbiome composition and function are associated with childhood IBS fructan-induced symptoms.<br><br>METHODS: Faecal samples were collected from 38 children aged 7-17 years with paediatric Rome III IBS, who previously completied a double-blind, randomised, placebo-controlled crossover (fructan vs maltodextrin) trial. Fructan sensitivity was defined as an increase of ≥30% in abdominal pain frequency during the fructan diet. Gut microbial composition was determined via 16Sv4 rDNA sequencing. LEfSe evaluated taxonomic composition differences. Tax4Fun2 predicted microbial fructan metabolic pathways.<br><br>RESULTS: At baseline, 17 fructan-sensitive (vs 21 fructan-tolerant) subjects had lower alpha diversity (q < 0.05) and were enriched in the genus Holdermania. In contrast, fructan-tolerant subjects were enriched in 14 genera from the class Clostridia. During the fructan diet, fructan-sensitive (vs tolerant) subjects were enriched in both Agathobacter (P = 0.02) and Cyanobacteria (P = 0.0001). In contrast, fructan-tolerant subjects were enriched in three genera from the Clostridia class. Comparing the fructan vs maltodextrin diet, fructan-sensitive subjects had a significantly increased relative abundance of Bifidobacterium (P = 0.02) while fructan-tolerant subjects had increased Anaerostipes (P = 0.03) during the fructan diet. Only fructan-sensitive subjects had a trend towards increased predicted β-fructofuranosidase during the fructan vs maltodextrin diet.<br><br>CONCLUSIONS: Fructan-sensitive children with IBS have distinct gut microbiome signatures. These microbiome signatures differ both at baseline and in response to a fructan challenge.},
}
@article {pmid33313416,
year = {2020},
author = {Wang, Q and Feng, J and Zhang, J and Shi, L and Jin, Z and Liu, D and Wu, B and Chen, J},
title = {Diagnosis of complication in lung transplantation by TBLB + ROSE + mNGS.},
journal = {Open medicine (Warsaw, Poland)},
volume = {15},
number = {1},
pages = {968-980},
pmid = {33313416},
issn = {2391-5463},
abstract = {Lung transplantation is a potentially life-saving therapy for patients with terminal respiratory illnesses. Long-term survival is limited by the development of a variety of opportunistic infections and rejection. Optimal means of differential diagnosis of infection and rejection have not been established. With these challenges in mind, we tried to use transbronchial lung biopsy (TBLB) rapid on-site cytological evaluation (ROSE), metagenomic next-generation sequencing (mNGS), and routine histologic examination to timely distinguish infection and rejection, and accurately detect etiologic pathogens. We reviewed the medical records of all patients diagnosed with infection or rejection by these means from December 2017 to September 2018 in our center. We identified seven recipients whose clinical course was complicated by infection or rejection. Three patients were diagnosed with acute rejection, organizing pneumonia, and acute fibrinoid organizing pneumonia, respectively. Four of the seven patients were diagnosed with infections, including Pneumocystis carinii pneumonia, cytomegalovirus, Aspergillus, and bacterial pneumonia. These patients recovered after proper treatment. TBLB + ROSE + mNGS might be a good method to accurately detect etiologic pathogens, which may help us to facilitate the use of targeted and precision medicine therapy in postoperative complications and avoid unnecessary potential adverse effects of drugs.},
}
@article {pmid33312634,
year = {2020},
author = {Pérez-Díaz, MI and Zárate-Segura, P and Bermeo-Fernández, LA and Nirmalkar, K and Bastida-González, F and García-Mena, J and Jan-Roblero, J and Guerrero-Barajas, C},
title = {&quot;Bacterial consortium from hydrothermal vent sediments presents electrogenic activity achieved under sulfate reducing conditions in a microbial fuel cell&quot;.},
journal = {Journal of environmental health science &amp; engineering},
volume = {18},
number = {2},
pages = {1189-1205},
pmid = {33312634},
issn = {2052-336X},
abstract = {Purpose: The aim of the present work was to assess the electrogenic activity of bacteria from hydrothermal vent sediments achieved under sulfate reducing (SR) conditions in a microbial fuel cell design with acetate, propionate and butyrate as electron donors.<br><br>Methods: Two different mixtures of volatile fatty acids (VFA) were evaluated as the carbon source at two chemical oxygen demand (COD) proportions. The mixtures of VFA used were: acetate, propionate and butyrate COD: 3:0.5:0.5 (stage 1) and acetate - butyrate COD: 3.5:0.5 (stage 2). Periodical analysis of sulfate (SO4-2), sulfide (HS-) and COD were conducted to assess sulfate reduction (SR) and COD removal along with measurements of voltage and current to assess the global performance of the consortium in the system.<br><br>Results: Percentage of SR was of 97.5 ± 0.7 and 74.3 ± 1.5% for stage 1 and 2, respectively. The % COD removal was of 91 ± 2.1 and 75.3 ± 9.6 for stage 1 and 2, respectively. Although SR and COD removal were higher at stage 1, in regards of energy, stage 2 presented higher current and power densities and Coulombic efficiency as follows: 741.7 ± 30.5 μA/m2, 376 ± 34.4 μW/m2 and 5 ± 2.7%, whereas for stage 1 these values were: 419 ± 71 μA/m2, 52.7 ± 18 μW/m2 and 0.02%, respectively. A metagenomic analysis - stage 2 - in the anodic chamber, demonstrated that SR was due to Dethiosulfovibrionaceae (HA73), Desulfobacter and Desulfococcus and the electrogenic microorganisms were Planococcus, SHD-231, Proteiniclasticum, vadinCA02, and families Porphyromonadacea and Pseudomonadaceae.<br><br>Conclusions: It was demonstrated that microorganisms prevenient from hydrothermal vent sediments adapted to a microbial fuel cell system are able to generate electricity coupled to 74.3 ± 1.5 and 75.3 ± 9.6% of SR and COD removal respectively, with a mixture of acetate - butyrate.},
}
@article {pmid33312575,
year = {2020},
author = {Basim, Y and Mohebali, G and Jorfi, S and Nabizadeh, R and Ghadiri, A and Moghadam, MA and Soleymani, F and Fard, NJH},
title = {Comparison of performance and efficiency of four methods to extract genomic DNA from oil contaminated soils in southwestern of Iran.},
journal = {Journal of environmental health science &amp; engineering},
volume = {18},
number = {2},
pages = {463-468},
pmid = {33312575},
issn = {2052-336X},
abstract = {The wide spectrum of oil industry activities caused soil contaminants, as environmental concern in many areas of the world. Bioremediation of oily soils, as biological approach done by bacteria and fungi, is very important to eliminate this pollution. In this study four different metagenomic protocols for DNA extraction has been tested in order to sequence and identify the native bacterial species involved in remediation of oily soils. In this regard, 3 manual methods and a soil DNA extraction kit are used. In manual protocol, physical processes including the addition of silica beads and freezing samples by liquid nitrogen, chemical methods such as treating the lysozyme, and lysis buffer and proteinase K as biochemical methods were utilized for optimal extraction. Quality and quantity of the extracted DNA analyzed using Agarose gel electrophoresis and Picodrop respectively. Then, the 16S rdna gene of bacteria amplified through universal primer for preparing a genomic library by PCR. Results showed that the highest concentration and quality of extracted DNA was obtained by protocol D which was about 135 μg/ul and 260/230 = 2.2 respectively. Moreover, 500 bp fragment amplified perfectly by using DNA extracted through protocol D in the PCR test. Therefore, protocol D can be used as an appropriate and effective way in order to study the microbial population of oily soils using direct extraction of DNA.},
}
@article {pmid33312167,
year = {2020},
author = {Campbell, MA and Grice, K and Visscher, PT and Morris, T and Wong, HL and White, RA and Burns, BP and Coolen, MJL},
title = {Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {560336},
pmid = {33312167},
issn = {1664-302X},
abstract = {Microbial mat communities possess extensive taxonomic and functional diversity, which drive high metabolic rates and rapid cycling of major elements. Modern microbial mats occurring in hypersaline environments are considered as analogs to extinct geobiological formations dating back to ∼ 3.5 Gyr ago. Despite efforts to understand the diversity and metabolic potential of hypersaline microbial mats in Shark Bay, Western Australia, there has yet to be molecular analyses at the transcriptional level in these microbial communities. In this study, we generated metatranscriptomes for the first time from actively growing mats comparing the type of mat, as well as the influence of diel and seasonal cycles. We observed that the overall gene transcription is strongly influenced by microbial community structure and seasonality. The most transcribed genes were associated with tackling the low nutrient conditions by the uptake of fatty acids, phosphorus, iron, and nickel from the environment as well as with protective mechanisms against elevated salinity conditions and to prevent build-up of ammonium produced by nitrate reducing microorganisms. A range of pathways involved in carbon, nitrogen, and sulfur cycles were identified in mat metatranscriptomes, with anoxygenic photosynthesis and chemoautotrophy using the Arnon-Buchanan cycle inferred as major pathways involved in the carbon cycle. Furthermore, enrichment of active anaerobic pathways (e.g., sulfate reduction, methanogenesis, Wood-Ljungdahl) in smooth mats corroborates previous metagenomic studies and further advocates the potential of these communities as modern analogs of ancient microbialites.},
}
@article {pmid33311714,
year = {2020},
author = {Lee, KS and Pereira, FC and Palatinszky, M and Behrendt, L and Alcolombri, U and Berry, D and Wagner, M and Stocker, R},
title = {Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {33311714},
issn = {1750-2799},
support = {GBMF3783//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; P26127-B20//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P27831-B28//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P26127-B20//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P27831-B28//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 2019-04401//Vetenskapsrådet (Swedish Research Council)/ ; },
abstract = {Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question &quot;who does what?&quot; in complex microbial communities when coupled with fluorescence in situ hybridization or downstream 'omics' analyses. We have developed a platform for automated Raman-based sorting in which optical tweezers and microfluidics are used to sort individual cells of interest from microbial communities on the basis of their Raman spectra. This sorting of cells and their downstream DNA analysis, such as by mini-metagenomics or single-cell genomics, or cultivation permits a direct link to be made between the metabolic roles and the genomes of microbial cells within complex microbial communities, as well as targeted isolation of novel microbes with a specific physiology of interest. We describe a protocol from sample preparation through Raman-activated live cell sorting. Subsequent cultivation of sorted cells is described, whereas downstream DNA analysis involves well-established approaches with abundant methods available in the literature. Compared with manual sorting, this technique provides a substantially higher throughput (up to 500 cells per h). Furthermore, the platform has very high sorting accuracy (98.3 ± 1.7%) and is fully automated, thus avoiding user biases that might accompany manual sorting. We anticipate that this protocol will empower in particular environmental and host-associated microbiome research with a versatile tool to elucidate the metabolic contributions of microbial taxa within their complex communities. After a 1-d preparation of cells, sorting takes on the order of 4 h, depending on the number of cells required.},
}
@article {pmid33310751,
year = {2020},
author = {He, X and Gao, J and Peng, L and Hu, T and Wan, Y and Zhou, M and Zhen, P and Cao, H},
title = {Bacterial O-GlcNAcase genes abundance decreases in ulcerative colitis patients and its administration ameliorates colitis in mice.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2020-322468},
pmid = {33310751},
issn = {1468-3288},
abstract = {OBJECTIVE: O-linked N-acetylglucosaminylation (O-GlcNAcylation), controlled by O-GlcNAcase (OGA) and O-GlcNAc transferase (OGT), is an important post-translational modification of eukaryotic proteins and plays an essential role in regulating gut inflammation. Gut microbiota encode various enzymes involved in O-GlcNAcylation. However, the characteristics, abundance and function of these enzymes are unknown.<br><br>DESIGN: We first investigated the structure and taxonomic distribution of bacterial OGAs and OGTs. Then, we performed metagenomic analysis to explore the OGA genes abundance in health samples and different diseases. Finally, we employed in vitro and in vivo experiments to determine the effects and mechanisms of bacterial OGAs to hydrolyse O-GlcNAcylated proteins in host cells and suppress inflammatory response in the gut.<br><br>RESULTS: We found OGAs, instead of OGTs, are enriched in Bacteroidetes and Firmicutes, the major bacterial divisions in the human gut. Most bacterial OGAs are secreted enzymes with the same conserved catalytic domain as human OGAs. A pooled analysis on 1999 metagenomic samples encompassed six diseases revealed that bacterial OGA genes were conserved in healthy human gut with high abundance, and reduced exclusively in ulcerative colitis. In vitro studies showed that bacterial OGAs could hydrolyse O-GlcNAcylated proteins in host cells, including O-GlcNAcylated NF-κB-p65 subunit, which is important for activating NF-κB signalling. In vivo studies demonstrated that gut bacteria-derived OGAs could protect mice from chemically induced colonic inflammation through hydrolysing O-GlcNAcylated proteins.<br><br>CONCLUSION: Our results reveal a previously unrecognised enzymatic activity by which gut microbiota influence intestinal physiology and highlight bacterial OGAs as a promising therapeutic strategy in colonic inflammation.},
}
@article {pmid33310720,
year = {2020},
author = {Wang, C and Song, Y and Tang, N and Zhang, G and Leclercq, SO and Feng, J},
title = {The shared resistome of human and pig microbiota is mobilized by distinct genetic elements.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.01910-20},
pmid = {33310720},
issn = {1098-5336},
abstract = {The extensive use of antibiotics in hospitals and in the animal breeding industry has promoted antibiotic resistance in bacteria, which resulted in the emergence of a large number of antibiotic resistance genes in the intestinal tract of human and farmed animals. Genetic exchange of resistance genes between the two ecosystems is now well documented for pathogenic bacteria, but the repertoire of shared resistance genes in the commensal bacterial community and by which genetic modules they are disseminated are still unclear. By analyzing metagenomics data of human and pig intestinal samples both collected in Shenzhen, China, a set of 27 highly prevalent antibiotic resistance genes was found to be shared between human and pig intestinal microbiota. The mobile genetic context for 11 of these core antibiotic resistance genes could be identified by mining their carrying scaffolds constructed from the two datasets, leading to the detection of seven integrative and conjugative/mobilizable elements and two IS-related transposons. The comparison of the relative abundances between these detected mobile genetic elements and their associated antibiotic resistance genes revealed that for many genes, the estimated contribution of the mobile elements to the gene abundance differs strikingly depending on the host. These findings indicate that although some antibiotic resistance genes are ubiquitous across microbiota of human and pig populations, they probably relied on different genetic elements for their dissemination within each population.IMPORTANCE There is growing concern that antibiotic resistance genes could spread from the husbandry environment to human pathogens through dissemination mediated by mobile genetic elements. In this study, we investigated the contribution of mobile genetic elements to the abundance of highly prevalent antibiotic resistance genes found in commensal bacteria of both human and pig intestinal microbiota originating from the same region. Our results reveal that for most of these antibiotic resistance genes, the abundance is not explained by the same mobile genetic element in each host, suggesting that the human and pig microbial communities promoted a different set of mobile genetic carriers for the same antibiotic resistance genes. These results deepen our understanding of the dissemination of antibiotic resistance genes among and between human and pig gut microbiota.},
}
@article {pmid33310436,
year = {2020},
author = {Bal Krishna, KC and Sathasivan, A and Ginige, MP},
title = {An assessment of the persistence of putative pathogenic bacteria in chloraminated water distribution systems.},
journal = {Water research},
volume = {190},
number = {},
pages = {116677},
doi = {10.1016/j.watres.2020.116677},
pmid = {33310436},
issn = {1879-2448},
abstract = {This study investigated how a chloramine loss and nitrifying conditions influenced putative pathogenic bacterial diversity in bulk water and biofilm of a laboratory- and a full-scale chloraminated water distribution systems. Fifty-four reference databases containing full-length 16S rRNA gene sequences obtained from the National Centre for Biotechnology Information database were prepared to represent fifty-four pathogenic bacterial species listed in the World Health Organisation and Australian Drinking Water Quality Guidelines. When 16S rRNA gene sequences of all samples were screened against the fifty-four reference pathogenic databases, a total of thirty-one putative pathogenic bacteria were detected in both laboratory- and full-scale systems where total chlorine residuals ranged between 0.03 - 2.2 mg/L. Pathogenic bacterial species Mycolicibacterium fortuitum and Pseudomonas aeruginosa were noted in all laboratory (i.e. in bulk water and biofilm) and in bulk water of full-scale samples and Mycolicibacterium fortuitum dominated when chloramine residuals were high. Other different pathogenic bacterial species were observed dominant with decaying chloramine residuals. This study for the first time reports the diverse abundance of putative pathogenic bacteria resilient towards chloramine and highlights that metagenomics surveillance of drinking water can serve as a rapid assessment and an early warning of outbreaks of a large number of putative pathogenic bacteria.},
}
@article {pmid33310371,
year = {2021},
author = {Murillo, J and Villegas, LM and Ulloa-Murillo, LM and Rodríguez, AR},
title = {Recent trends on omics and bioinformatics approaches to study SARS-CoV-2: A bibliometric analysis and mini-review.},
journal = {Computers in biology and medicine},
volume = {128},
number = {},
pages = {104162},
doi = {10.1016/j.compbiomed.2020.104162},
pmid = {33310371},
issn = {1879-0534},
abstract = {BACKGROUND: The successful sequencing of SARS-CoV-2 cleared the way for the use of omics technologies and integrative biology research for combating the COVID-19 pandemic. Currently, many research groups have slowed down their respective projects to concentrate efforts in the study of the biology of SARS-CoV-2. In this bibliometric analysis and mini-review, we aimed to describe how computational methods or omics approaches were used during the first months of the COVID-19 pandemic.<br><br>METHODS: We analyzed bibliometric data from Scopus, BioRxiv, and MedRxiv (dated June 19th, 2020) using quantitative and knowledge mapping approaches. We complemented our analysis with a manual process of carefully reading the selected articles to identify either the omics or bioinformatic tools used and their purpose.<br><br>RESULTS: From a total of 184 articles, we found that metagenomics and transcriptomics were the main sources of data to perform phylogenetic analysis aimed at corroborating zoonotic transmission, identifying the animal origin and taxonomic allocation of SARS-CoV-2. Protein sequence analysis, immunoinformatics and molecular docking were used to give insights about SARS-CoV-2 targets for drug and vaccine development. Most of the publications were from China and USA. However, China, Italy and India covered the top 10 most cited papers on this topic.<br><br>CONCLUSION: We found an abundance of publications using omics and bioinformatics approaches to establish the taxonomy and animal origin of SARS-CoV-2. We encourage the growing community of researchers to explore other lesser-known aspects of COVID-19 such as virus-host interactions and host response.},
}
@article {pmid33310320,
year = {2020},
author = {Sun, Y and Sun, J and Nghiem, AA and Bostick, BC and Ellis, T and Han, L and Li, Z and Liu, S and Han, S and Zhang, M and Xia, Y and Zheng, Y},
title = {Reduction of iron (hydr)oxide-bound arsenate: Evidence from high depth resolution sampling of a reducing aquifer in Yinchuan Plain, China.},
journal = {Journal of hazardous materials},
volume = {406},
number = {},
pages = {124615},
doi = {10.1016/j.jhazmat.2020.124615},
pmid = {33310320},
issn = {1873-3336},
abstract = {Sediment in fluvial-deltaic plains with high-As groundwater is heterogenous but its characterization of As and Fe oxidation states lacks resolution, and is rarely attempted for aqueous and solid phases simultaneously. Here, we pair high-resolution (> 1 sample/meter) Fe extended fine-structure spectroscopy (EXAFS, n = 40) and As X-ray absorption near-edge spectroscopy (XANES, n = 49) with groundwater composition and metagenomics measurements for two sediment cores and their associated wells (n = 8) from the Yinchuan Plain in northwest China. At shallower depths, nitrate and Mn/Fe reducing sediment zones are fine textured, contain 9.6 ± 5.6 mg kg-1 of As(V) and 2.3 ± 2.7 mg kg-1 of As(III) with 9.1 ± 8.1 g kg-1 of Fe(III) (hydr)oxides, with bacterial genera capable of As and Fe reduction identified. In four deeper 10-m sections, sulfate-reducing sediments are coarser and contain 2.6 ± 1.3 mg kg-1 of As(V) and 1.1 ± 1.0 mg kg-1 of As(III) with 3.2 ± 2.6 g kg-1 of Fe(III) (hydr)oxides, even though groundwater As concentrations can exceed 200 μg/L, mostly as As(III). Super-enrichment of sediment As (42-133 mg kg-1, n = 7) at shallower depth is due to redox trapping during past groundwater discharge. Active As and Fe reduction is supported by the contrast between the As(III)-dominated groundwater and the As(V)-dominated sediment, and by the decreasing sediment As(V) and Fe(III) (hydr)oxides concentrations with depth.},
}
@article {pmid33310237,
year = {2020},
author = {Yu, H and Ye, X and Feng, L and Yang, J and Lan, Z and Ren, C and Zhu, W and Yang, G and Zhou, J},
title = {Dynamics of denitrification performance and denitrifying community under high-dose acute oxytetracycline exposure and various biorecovery strategies in polycaprolactone-supported solid-phase denitrification.},
journal = {Journal of environmental management},
volume = {279},
number = {},
pages = {111763},
doi = {10.1016/j.jenvman.2020.111763},
pmid = {33310237},
issn = {1095-8630},
abstract = {Solid-phase denitrification (SPD) is a promising technology for nitrate-rich water purification. This study aimed to examine the variation in denitrification performance and denitrifying community under high-dose acute oxytetracycline (OTC) exposure and various biorecovery strategies. The denitrification performance was impaired significantly after one-day OTC shock at 50 mg L-1 in a continuous-flow SPD system supported by a polycaprolactone (PCL) carrier but could rapidly recover without the addition of OTC. When 50 mg L-1 OTC stress was applied for a longer time in the batch tests, a natural recovery period of more than 20 days was required to reach more than 95% nitrate reduction. Under the same conditions, the addition of both mature biofilm-attached PCL carrier and fresh biofilm-free PCL carrier significantly shortened the recovery time for efficient nitrate reduction, mainly due to the increase in organic availability from the PCL carriers. However, the composition of the microbial community notably changed due to the effects of OTC according to high-throughput sequencing and metagenomic analysis. Genes encoding NAR and NIR were much more sensitive than those encoding NOR and NOS to OTC shock. Tetracycline resistance gene (TRG) enrichment was 15.86% higher in the biofilm that experienced short-term OTC shock than in the control biofilm in the continuous-flow SPD system.},
}
@article {pmid33310084,
year = {2020},
author = {Galipeau, HJ and Caminero, A and Turpin, W and Bermudez-Brito, M and Santiago, A and Libertucci, J and Constante, M and Raygoza Garay, JA and Rueda, G and Armstrong, S and Clarizio, A and Smith, MI and Surette, MG and Bercik, P and , and Croitoru, K and Verdu, EF},
title = {Novel fecal biomarkers that precede clinical diagnosis of ulcerative colitis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2020.12.004},
pmid = {33310084},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: Altered gut microbiota composition and function have been associated with inflammatory bowel diseases (IBD) including ulcerative colitis (UC), but causality and mechanisms remain unknown.<br><br>METHODS: We applied 16S rRNA gene sequencing, shotgun metagenomic sequencing, in vitro functional assays and gnotobiotic colonizations to define the microbial composition and function in fecal samples obtained from a cohort of healthy individuals at-risk for IBD (pre-UC) that later developed UC (post-UC), and matched healthy controls (HC).<br><br>RESULTS: Microbiota composition of post-UC subjects was different from HC and pre-UC; however, functional analysis revealed increased fecal proteolytic and elastase activity before UC onset. Metagenomics identified over 22,000 gene families that were significantly different between HC, pre-UC and post-UC samples. Of these, 237 related to proteases and peptidases, suggesting a bacterial component to the pre-UC proteolytic signature. Elastase activity inversely correlated with the relative abundance of Adlercreutzia and other potentially beneficial taxa, and directly correlated with known proteolytic taxa, such as Bacteroides vulgatus. High elastase activity was confirmed in Bacteroides isolates from fecal samples. Bacterial contribution and functional significance of the proteolytic signature were investigated in germ-free adult mice and in dams colonized with HC, pre-UC or post-UC microbiota. Mice colonized with or born from pre-UC colonized dams developed higher fecal proteolytic activity and an inflammatory immune tone compared with HC colonized mice.<br><br>CONCLUSIONS: We have identified increased fecal proteolytic activity that precedes the clinical diagnosis of UC and associates with gut microbiota changes. This proteolytic signature may constitute a non-invasive biomarker of inflammation to monitor at-risk populations that can be targeted therapeutically with anti-proteases.},
}
@article {pmid33309006,
year = {2020},
author = {Skov, J and Kristiansen, K and Jespersen, J and Olesen, P},
title = {Status and perspectives of biomarker validation for diagnosis, stratification, and treatment.},
journal = {Public health},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.puhe.2020.11.002},
pmid = {33309006},
issn = {1476-5616},
abstract = {OBJECTIVES: The aim of this study was to discuss the status of and perspective for biomarker validation in view of the challenges imposed on national healthcare systems due to an increasing number of citizens with chronic diseases and new expensive drugs with effects that are sometimes poorly documented. The demand for a paradigm shift toward stratification of patients or even 'personalized medicine' (PM) is rising, and the implementation of such novel strategies has the potential to increase patient outcomes and cost efficiency of treatments. The implementation of PM depends on relevant and reliable biomarkers correlated to disease states, prognosis, or effect of treatment. Beyond biomarkers of disease, personalized prevention strategies (such as individualized nutrition guidance) are likely to depend on novel biomarkers.<br><br>STUDY DESIGN: We discuss the current status of the use of biomarkers and the need for standardization and integration of biomarkers based on multi-omics approaches.<br><br>METHODS: We present representative cases from laboratory medicine, oncology, and nutrition, where present and emerging biomarkers have or may present opportunities for PM or prevention.<br><br>RESULTS: Biomarkers vary greatly in complexity, from single genomic mutations to metagenomic analyses of the composition of the gut microbiota and comprehensive analyses of metabolites, metabolomics. Using biomarkers for decision-making has previously often relied on measurements of single biomolecules. The current development now moves toward the use of multiple biomarkers requiring the use of machine learning or artificial intelligence. Still, the usefulness of biomarkers is often challenged by suboptimal validation, and the discovery of new biomarkers moves much faster than standardization efforts. To reap the potential benefits of personalization of treatment and prevention, healthcare systems and regulatory authorities need to focus on validation and standardization of biomarkers.<br><br>CONCLUSION: There is a great public health need for better understanding of the usefulness, but also limitations, of biomarkers among policy makers, clinicians, and scientists, and efforts securing effective validation are key to the future use of novel sets of complex biomarkers.},
}
@article {pmid33308279,
year = {2020},
author = {Yulandi, A and Suwanto, A and Waturangi, DE and Wahyudi, AT},
title = {Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh.},
journal = {BMC research notes},
volume = {13},
number = {1},
pages = {562},
pmid = {33308279},
issn = {1756-0500},
abstract = {OBJECTIVE: Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used to profile the microbial community from fermented food samples. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in estimating microbial community composition. As potential paraprobiotics sources, a comprehensive profiling study of tempeh microbial ecology could contribute to tempeh product development. This study employed a shotgun metagenomic approach, where metagenome fragments from tempeh samples were sequenced directly for taxonomic and functional profiling analysis.<br><br>RESULTS: Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the shotgun metagenomic analysis in all tempeh samples. In terms of composition, this shotgun metagenomic study revealed that Proteobacteria was the most abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed gene based on this metagenomic analysis. The metagenome-assembled genomes (MAGs) results from the binning pipeline could reveal almost complete whole genome sequence of Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii.},
}
@article {pmid33308267,
year = {2020},
author = {Accorsi, EK and Franzosa, EA and Hsu, T and Joice Cordy, R and Maayan-Metzger, A and Jaber, H and Reiss-Mandel, A and Kline, M and DuLong, C and Lipsitch, M and Regev-Yochay, G and Huttenhower, C},
title = {Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {301},
pmid = {33308267},
issn = {1474-760X},
support = {R21AI112991//National Institute of Allergy and Infectious Diseases/ ; T32AI007535//National Institute of Allergy and Infectious Diseases/ ; 3-00000-5622//Office of the Chief Scientist, Ministry of Health/ ; 1590/09//Israel Science Foundation/ ; 1658/15//Israel Science Foundation/ ; },
abstract = {BACKGROUND: Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage. It is thus important to identify ecological or functional genetic elements within the maternal or infant nasal microbiomes that influence S. aureus acquisition and retention in early life.<br><br>RESULTS: We recruited 36 mother-infant pairs and profiled a subset of monthly longitudinal nasal samples from the first year after birth using shotgun metagenomic sequencing. The infant nasal microbiome is highly variable, particularly within the first 2 months. It is weakly influenced by maternal nasal microbiome composition, but primarily shaped by developmental and external factors, such as daycare. Infants display distinctive patterns of S. aureus carriage, positively associated with Acinetobacter species, Streptococcus parasanguinis, Streptococcus salivarius, and Veillonella species and inversely associated with maternal Dolosigranulum pigrum. Furthermore, we identify a gene family, likely acting as a taxonomic marker for an unclassified species, that is significantly anti-correlated with S. aureus in infants and mothers. In gene content-based strain profiling, infant S. aureus strains are more similar to maternal strains.<br><br>CONCLUSIONS: This improved understanding of S. aureus colonization is an important first step toward the development of novel, ecological therapies for controlling S. aureus carriage.},
}
@article {pmid33308114,
year = {2020},
author = {Wu, X and Chen, X and Lyu, X and Zheng, H},
title = {Advances in Microbiome Detection Technologies and Application in Antirheumatic Drug Design.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/1381612826666201211114609},
pmid = {33308114},
issn = {1873-4286},
abstract = {Rheumatic diseases are a kind of chronic inflammatory and autoimmune disease affecting the connection or supporting structures of the human body, such as the most common diseases Ankylosing spondylitis (AS), gout and Systemic lupus erythematosus (SLE). Although the precise etiology and pathogenesis of the different types of rheumatic diseases remain mostly unknown, it is now commonly believed that these diseases are attributed to some complex interactions between genetics and environmental factors, especially the gut microbiome. Altered microbiome showed clinical improvement in disease symptoms and partially restored to normality after prescribing disease-modifying antirheumatic drugs (DMARDs) or other treatment strategies. Recent advances in next-generation sequencing-based microbial profiling technology, especially metagenomics, have identified alteration of the composition and function of the gut microbiota in patients. Clinical and experimental data suggest dysbiosis may play a pivotal role in the pathogenesis of these diseases. In this paper, we provide a brief review of the advances in the microbial profiling technology and up-todate resources for accurate taxonomic assignment of metagenomic reads, which is a key step for metagenomics studies. In addition, we review the altered gut microbiota signatures that have been reported so far across various studies, upon which diagnostics classification models can be constructed, and the drug-induced regulation of the host microbiota can be used to control disease progression and symptoms.},
}
@article {pmid33307023,
year = {2020},
author = {Britton, RA and Hoffmann, DE and Khoruts, A},
title = {Probiotics and the Microbiome: How Can We Help Patients Make Sense of Probiotics?.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2020.11.047},
pmid = {33307023},
issn = {1528-0012},
abstract = {The notion of probiotics as microbes that confer health benefits has its origins in the speculative ideas that are more than a century old, yet remain largely unsubstantiated by scientific evidence. The recent advances in microbiome science have highlighted the importance of intestinal microbes in human physiology and disease pathogenesis. These developments have provided a boost to the probiotics industry, which continues to experience exponential growth driven mainly by creative marketing. Consumers, patients, and most health care providers are not able to discern the underlying science or differentiate the permitted claims that promise vague health benefits from disease-specific claims reserved for drugs. No probiotic product has been able to satisfy the regulatory requirements to be categorized as a drug, a substance intended to cure, mitigate, or prevent disease. However, patients take probiotic products in the belief that they will help to treat their intestinal or systemic diseases. Thus far, the regulators have failed to create policies that would assist to inform the public in this area. In fact, the existing regulatory regime actually creates formidable barriers to research that could provide evidence for clinical efficacy of probiotic products. We propose a potential solution to this vexing problem, where a committee created through a partnership of academia, professional organizations, and industry, but free of potential conflicts of interest, would be charged with rigorous evaluation of specific probiotic products and the evidence in support of their different claims. Companies that would submit to this process would earn the trust of consumers and healthcare providers, as well as a distinction in the marketplace.},
}
@article {pmid33305509,
year = {2020},
author = {Alexyuk, M and Bogoyavlenskiy, A and Alexyuk, P and Moldakhanov, Y and Berezin, V and Digel, I},
title = {Epipelagic microbiome of the Small Aral Sea: Metagenomic structure and ecological diversity.},
journal = {MicrobiologyOpen},
volume = {},
number = {},
pages = {e1142},
doi = {10.1002/mbo3.1142},
pmid = {33305509},
issn = {2045-8827},
support = {AP05130916//Ministry of Education and Science of Kazakhstan/ ; AP05131106//Ministry of Education and Science of Kazakhstan/ ; },
abstract = {Microbial diversity studies regarding the aquatic communities that experienced or are experiencing environmental problems are essential for the comprehension of the remediation dynamics. In this pilot study, we present data on the phylogenetic and ecological structure of microorganisms from epipelagic water samples collected in the Small Aral Sea (SAS). The raw data were generated by massive parallel sequencing using the shotgun approach. As expected, most of the identified DNA sequences belonged to Terrabacteria and Actinobacteria (40% and 37% of the total reads, respectively). The occurrence of Deinococcus-Thermus, Armatimonadetes, Chloroflexi in the epipelagic SAS waters was less anticipated. Surprising was also the detection of sequences, which are characteristic for strict anaerobes-Ignavibacteria, hydrogen-oxidizing bacteria, and archaeal methanogenic species. We suppose that the observed very broad range of phylogenetic and ecological features displayed by the SAS reads demonstrates a more intensive mixing of water masses originating from diverse ecological niches of the Aral-Syr Darya River basin than presumed before.},
}
@article {pmid33304545,
year = {2020},
author = {Monleon-Getino, T and Frias-Lopez, J},
title = {A priori estimation of sequencing effort in complex microbial metatranscriptomes.},
journal = {Ecology and evolution},
volume = {10},
number = {23},
pages = {13382-13394},
pmid = {33304545},
issn = {2045-7758},
abstract = {Metatranscriptome analysis or the analysis of the expression profiles of whole microbial communities has the additional challenge of dealing with a complex system with dozens of different organisms expressing genes simultaneously. An underlying issue for virtually all metatranscriptomic sequencing experiments is how to allocate the limited sequencing budget while guaranteeing that the libraries have sufficient depth to cover the breadth of expression of the community. Estimating the required sequencing depth to effectively sample the target metatranscriptome using RNA-seq is an essential first step to obtain robust results in subsequent analysis and to avoid overexpansion, once the information contained in the library reaches saturation. Here, we present a method to calculate the sequencing effort using a simulated series of metatranscriptomic/metagenomic matrices. This method is based on an extrapolation rarefaction curve using a Weibull growth model to estimate the maximum number of observed genes as a function of sequencing depth. This approach allowed us to compute the effort at different confidence intervals and to obtain an approximate a priori effort based on an initial fraction of sequences. The analytical pipeline presented here may be successfully used for the in-depth and time-effective characterization of complex microbial communities, representing a useful tool for the microbiome research community.},
}
@article {pmid33304338,
year = {2020},
author = {Gaeta, NC and Bean, E and Miles, AM and de Carvalho, DUOG and Alemán, MAR and Carvalho, JS and Gregory, L and Ganda, E},
title = {A Cross-Sectional Study of Dairy Cattle Metagenomes Reveals Increased Antimicrobial Resistance in Animals Farmed in a Heavy Metal Contaminated Environment.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {590325},
pmid = {33304338},
issn = {1664-302X},
abstract = {The use of heavy metals in economic and social development can create an accumulation of toxic waste in the environment. High concentrations of heavy metals can damage human and animal health, lead to the development of antibiotic resistance, and possibly change in bovine microbiota. It is important to investigate the influence of heavy metals in food systems to determine potential harmful effects environmental heavy metal contamination on human health. Because of a mining dam rupture, 43 million cubic meters of iron ore waste flowed into the Doce river basin surrounding Mariana City, Brazil, in 2015. Following this environmental disaster, we investigated the consequences of long-term exposure to contaminated drinking water on the microbiome and resistome of dairy cattle. We identified bacterial antimicrobial resistance (AMR) genes in the feces, rumen fluid, and nasopharynx of 16 dairy cattle 4 years after the environmental disaster. Cattle had been continuously exposed to heavy metal contaminated water until sample collection (A) and compared them to analogous samples from 16 dairy cattle in an unaffected farm, 356 km away (B). The microbiome and resistome of farm A and farm B differed in many aspects. The distribution of genes present in the cattle's nasopharynx, rumen, and feces conferring AMR was highly heterogeneous, and most genes were present in only a few samples. The relative abundance and prevalence (presence/absence) of AMR genes were higher in farm A than in farm B. Samples from farm A had a higher prevalence (presence) of genes conferring resistance to multiple drugs, metals, biocides, and multi-compound resistance. Fecal samples had a higher relative abundance of AMR genes, followed by rumen fluid samples, and the nasopharynx had the lowest relative abundance of AMR genes detected. Metagenome functional annotation suggested that selective pressures of heavy metal exposure potentially skewed pathway diversity toward fewer, more specialized functions. This is the first study that evaluates the consequences of a Brazilian environmental accident with mining ore dam failure in the microbiome of dairy cows. Our findings suggest that the long-term persistence of heavy metals in the environment may result in differences in the microbiota and enrichment of antimicrobial-resistant bacteria. Our results also suggest that AMR genes are most readily detected in fecal samples compared to rumen and nasopharyngeal samples which had relatively lower bacterial read counts. Since heavy metal contamination has an effect on the animal microbiome, environmental management is warranted to protect the food system from hazardous consequences.},
}
@article {pmid33304336,
year = {2020},
author = {Laczi, K and Erdeiné Kis, Á and Szilágyi, Á and Bounedjoum, N and Bodor, A and Vincze, GE and Kovács, T and Rákhely, G and Perei, K},
title = {New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {590049},
pmid = {33304336},
issn = {1664-302X},
abstract = {The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.},
}
@article {pmid33304333,
year = {2020},
author = {Alves, JI and Visser, M and Arantes, AL and Nijsse, B and Plugge, CM and Alves, MM and Stams, AJM and Sousa, DZ},
title = {Effect of Sulfate on Carbon Monoxide Conversion by a Thermophilic Syngas-Fermenting Culture Dominated by a Desulfofundulus Species.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {588468},
pmid = {33304333},
issn = {1664-302X},
abstract = {A syngas-degrading enrichment culture, culture T-Syn, was dominated by a bacterium closely related to Desulfofundulus australicus strain AB33T (98% 16S rRNA gene sequence identity). Culture T-Syn could convert high CO concentrations (from pCO ≈ 34 kPa to pCO ≈ 170 kPa), both in the absence and in the presence of sulfate as external electron acceptor. The products formed from CO conversion were H2 and acetate. With sulfate, a lower H2/acetate ratio was observed in the product profile, but CO conversion rates were similar to those in the absence of sulfate. The ability of D. australicus strain AB33T to use CO was also investigated. D. australicus strain AB33T uses up to 40% CO (pCO ≈ 68 kPa) with sulfate and up to 20% CO (pCO ≈ 34 kPa) without sulfate. Comparison of the metagenome-assembled genome (MAG) of the Desulfofundulus sp. from T-Syn culture with the genome of D. australicus strain AB33T revealed high similarity, with an ANI value of 99% and only 32 unique genes in the genome of the Desulfofundulus sp. T-Syn. So far, only Desulfotomaculum nigrificans strain CO-1-SRB had been described to grow with CO with and without sulfate. This work further shows the carboxydotrophic potential of Desulfofundulus genus for CO conversion, both in sulfate-rich and low-sulfate environments.},
}
@article {pmid33304326,
year = {2020},
author = {Song, K},
title = {Classifying the Lifestyle of Metagenomically-Derived Phages Sequences Using Alignment-Free Methods.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {567769},
pmid = {33304326},
issn = {1664-302X},
abstract = {Phages are viruses that infect bacteria. The phages can be classified into two different categories based on their lifestyles: temperate and lytic. Now, the metavirome can generate a large number of fragments from the viral genomic sequences of entire environmental community, which makes it impossible to determine their lifestyles through experiments. Thus, there is a need to development computational methods for annotating phage contigs and making prediction of their lifestyles. Alignment-based methods for classifying phage lifestyle are limited by incomplete assembled genomes and nucleotide databases. Alignment-free methods based on the frequencies of k-mers were widely used for genome and metagenome comparison which did not rely on the completeness of genome or nucleotide databases. To mimic fragmented metagenomic sequences, the temperate and lytic phages genomic sequences were split into non-overlapping fragments with different lengths, then, I comprehensively compared nine alignment-free dissimilarity measures with a wide range of choices of k-mer length and Markov orders for predicting the lifestyles of these phage contigs. The dissimilarity measure, d 2 S , performed better than other dissimilarity measures for classifying the lifestyles of phages. Thus, I propose that the alignment-free method, d 2 S , can be used for predicting the lifestyles of phages which derived from the metagenomic data.},
}
@article {pmid33303873,
year = {2020},
author = {Yap, M and Feehily, C and Walsh, CJ and Fenelon, M and Murphy, EF and McAuliffe, FM and van Sinderen, D and O'Toole, PW and O'Sullivan, O and Cotter, PD},
title = {Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21665},
pmid = {33303873},
issn = {2045-2322},
support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; },
abstract = {Shotgun metagenomic sequencing is a valuable tool for the taxonomic and functional profiling of microbial communities. However, this approach is challenging in samples, such as milk, where a low microbial abundance, combined with high levels of host DNA, result in inefficient and uneconomical sequencing. Here we evaluate approaches to deplete host DNA or enrich microbial DNA prior to sequencing using three commercially available kits. We compared the percentage of microbial reads obtained from each kit after shotgun metagenomic sequencing. Using bovine and human milk samples, we determined that host depletion with the MolYsis complete5 kit significantly improved microbial sequencing depth compared to other approaches tested. Importantly, no biases were introduced. Additionally, the increased microbial sequencing depth allowed for further characterization of the microbiome through the generation of metagenome-assembled genomes (MAGs). Furthermore, with the use of a mock community, we compared three common classifiers and determined that Kraken2 was the optimal classifier for these samples. This evaluation shows that microbiome analysis can be performed on both bovine and human milk samples at a much greater resolution without the need for more expensive deep-sequencing approaches.},
}
@article {pmid33303662,
year = {2020},
author = {Martinez, JN and Kawai, S and Saini, MK and Tank, M and Hanada, S and Thiel, V},
title = {Draft Genome Sequence of a Filamentous Anoxygenic Phototrophic Bacterium, &quot;Candidatus Roseilinea sp. Strain NK_OTU-006,&quot; Recovered from Metagenomic Data of a Hot Spring Microbial Mat.},
journal = {Microbiology resource announcements},
volume = {9},
number = {50},
pages = {},
pmid = {33303662},
issn = {2576-098X},
abstract = {We report here the metagenome-assembled draft genome of an uncultured filamentous anoxygenic phototroph of the phylum Chloroflexota (formerly Chloroflexi), &quot;Candidatus Roseilinea sp. strain NK_OTU-006,&quot; recovered from hot spring-associated microbial mats. The 3.6-Mb genome is estimated to be 94% complete and comprises 117 contigs encoding 3,203 predicted genes, including a full-length rRNA operon.},
}
@article {pmid33302990,
year = {2020},
author = {Chen, JC and Tyler, AD},
title = {Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data.},
journal = {Biology direct},
volume = {15},
number = {1},
pages = {29},
pmid = {33302990},
issn = {1745-6150},
abstract = {BACKGROUND: The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately when the origin has been previously sampled. Using metagenomic datasets provided by the 2019 CAMDA challenge, we evaluated the influence of variable technical, analytical and machine learning approaches for result interpretation and novel source prediction.<br><br>RESULTS: Comparison between 16S rRNA amplicon and shotgun sequencing approaches as well as metagenomic analytical tools showed differences in normalized microbial abundance, especially for organisms present at low abundance. Shotgun sequence data analyzed using Kraken2 and Bracken, for taxonomic annotation, had higher detection sensitivity. As classification models are limited to labeling pre-trained origins, we took an alternative approach using Lasso-regularized multivariate regression to predict geographic coordinates for comparison. In both models, the prediction errors were much higher in Leave-1-city-out than in 10-fold cross validation, of which the former realistically forecasted the increased difficulty in accurately predicting samples from new origins. This challenge was further confirmed when applying the model to a set of samples obtained from new origins. Overall, the prediction performance of the regression and classification models, as measured by mean squared error, were comparable on mystery samples. Due to higher prediction error rates for samples from new origins, we provided an additional strategy based on prediction ambiguity to infer whether a sample is from a new origin. Lastly, we report increased prediction error when data from different sequencing protocols were included as training data.<br><br>CONCLUSIONS: Herein, we highlight the capacity of predicting sample origin accurately with pre-trained origins and the challenge of predicting new origins through both regression and classification models. Overall, this work provides a summary of the impact of sequencing technique, protocol, taxonomic analytical approaches, and machine learning approaches on the use of metagenomics for prediction of sample origin.},
}
@article {pmid33302682,
year = {2020},
author = {Zhang, M and Zhou, H and Xu, S and Liu, D and Cheng, Y and Gao, B and Li, X and Chen, J},
title = {The gut microbiome can be used to predict the gastrointestinal response and efficacy of lung cancer patients undergoing chemotherapy.},
journal = {Annals of palliative medicine},
volume = {9},
number = {6},
pages = {4211-4227},
doi = {10.21037/apm-20-2183},
pmid = {33302682},
issn = {2224-5839},
abstract = {BACKGROUND: Lung cancer has the highest incidence and mortality rate of any cancer worldwide. Platinum-based combination chemotherapy is still the standard treatment for advanced lung cancer. However, the clinical efficacy of this treatment can be affected by its adverse reactions, especially gastrointestinal mucositis. The adverse reactions often lead to delayed and reduced medication. The role played by gut microbiome in the treatment of cancer is becoming clearer, and evidence suggests that regulation of the gut microbiome may affect the response to multiple types of cancer treatment.<br><br>METHODS: Sixty lung cancer patients who received chemotherapy for the first time and 17 healthy subjects were enrolled in this study. A metagenomic analysis of 137 fecal samples was performed using next-generation sequencing technology.<br><br>RESULTS: The relative abundance of Eubacterium, Ruminococcus, and Faecalibacterium was higher in the lung cancer patients than in the healthy subjects; however, the relative abundance of Prevotella, Streptococcus, Enterococcus, and Roseburia showed the opposite result. The relative abundance of each gut microbiome changed significantly during chemotherapy. At the phylum level, the relative abundance of Firmicutes and Euryarchaeota was dramatically increased after chemotherapy. Lung cancer patients with a higher relative abundance of a particular bacterial genus, such as Prevotella, Megamonas, Streptococcus, Faecalibacterium, Roseburia, Parabacteroides, Coprococcus, Oscillibacter, Dorea, or Chlamydia, at baseline were more likely to experience gastrointestinal reactions. These results show that the intestinal flora can play a role in predicting the effect of chemotherapy in lung cancer patients.<br><br>CONCLUSIONS: The gut microbiome of patients with lung cancer differs from those of healthy people. The results of this study suggest that Ruminococcus and Eubacterium may be related to the occurrence and development of lung cancer. The gut microbiome of lung cancer patients changes significantly after treatment with cytotoxic drugs, which may be associated with the gastrointestinal reaction caused by chemotherapy. The gut microbiome also can be used to predict the efficacy of chemotherapy in lung cancer patients.},
}
@article {pmid33302422,
year = {2020},
author = {Hause, BM and Nelson, E and Christopher-Hennings, J},
title = {Novel and Diverse Non-Rabies Rhabdoviruses Identified in Bats with Human Exposure, South Dakota, USA.},
journal = {Viruses},
volume = {12},
number = {12},
pages = {},
pmid = {33302422},
issn = {1999-4915},
mesh = {Animals ; COVID-19/virology ; Chiroptera/*virology ; Female ; Genotype ; Humans ; Metagenomics ; Mice ; *Phylogeny ; Rabies virus ; Rhabdoviridae/*classification/isolation &amp; purification ; South Dakota ; Viral Zoonoses/transmission ; },
abstract = {Bats are a host and reservoir for a large number of viruses, many of which are zoonotic. In North America, the big brown bat (Eptesicus fuscus) is widely distributed and common. Big brown bats are a known reservoir for rabies virus, which, combined with their propensity to roost in human structures, necessitates testing for rabies virus following human exposure. The current pandemic caused by severe acute respiratory syndrome coronavirus 2, likely of bat origin, illustrates the need for continued surveillance of wildlife and bats for potentially emerging zoonotic viruses. Viral metagenomic sequencing was performed on 39 big brown bats and one hoary bat submitted for rabies testing due to human exposure in South Dakota. A new genotype of American bat vesiculovirus was identified in seven of 17 (41%) heart and lung homogenates at high levels in addition to two of 23 viscera pools. A second rhabdovirus, Sodak rhabdovirus 1 (SDRV1), was identified in four of 23 (17%) viscera pools. Phylogenetic analysis placed SDRV1 in the genus Alphanemrhavirus, which includes two recognized species that were identified in nematodes. Finally, a highly divergent rhabdovirus, Sodak rhabdovirus 2 (SDRV2), was identified in two of 23 (8.7%) big brown bats. Phylogenetic analysis placed SDRV2 as ancestral to the dimarhabdovirus supergroup and Lyssavirus. Intracranial inoculation of mouse pups with rhabdovirus-positive tissue homogenates failed to elicit clinical disease. Further research is needed to determine the zoonotic potential of these non-rabies rhabdoviruses.},
}
@article {pmid33302408,
year = {2020},
author = {Luque, A and Benler, S and Lee, DY and Brown, C and White, S},
title = {The Missing Tailed Phages: Prediction of Small Capsid Candidates.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33302408},
issn = {2076-2607},
support = {Award 1951678//National Science Foundation/ ; },
abstract = {Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common icosahedral capsid architectures T = 1 and T = 3 is puzzling. Here, we extracted geometrical features from high-resolution tailed phage capsid reconstructions and built a statistical model based on physical principles to predict the capsid diameter and genome length of the missing small-tailed phage capsids. We applied the model to 3348 isolated tailed phage genomes and 1496 gut metagenome-assembled tailed phage genomes. Four isolated tailed phages were predicted to form T = 3 icosahedral capsids, and twenty-one metagenome-assembled tailed phages were predicted to form T < 3 capsids. The smallest capsid predicted was a T = 4/3 ≈ 1.33 architecture. No tailed phages were predicted to form the smallest icosahedral architecture, T = 1. We discuss the feasibility of the missing T = 1 tailed phage capsids and the implications of isolating and characterizing small-tailed phages for viral evolution and phage therapy.},
}
@article {pmid33302189,
year = {2020},
author = {Shi, Z and Zhao, R and Wan, J and Li, B and Shen, Y and Zhang, S and Luo, G},
title = {Metagenomic analysis reveals the fate of antibiotic resistance genes in two-stage and one-stage anaerobic digestion of waste activated sludge.},
journal = {Journal of hazardous materials},
volume = {406},
number = {},
pages = {124595},
doi = {10.1016/j.jhazmat.2020.124595},
pmid = {33302189},
issn = {1873-3336},
abstract = {Waste activated sludge (WAS) from wastewater treatment plants is an important reservoir of antibiotic resistance genes (ARGs). The fate of ARGs in this process was not revealed previously. The present study applied metagenomic approach to examine the occurrence and fate of ARGs in thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM), by comparison with mesophilic alkaline fermentation followed by mesophilic anaerobic digestion (MM) and one-stage mesophilic anaerobic digestion (M) process. The removal efficiency of two-stage anaerobic digestion (AD) to total ARGs is higher than that of one-stage AD. The hydrogen and methane production stages of two-stage AD processes have dissimilar impact on the fate of ARGs. Macrolide, lincosamide, and streptogramin (MLS) resistance genes were enriched, especially in the hydrogen production reactors of TM and MM processes. Statistical analysis of metagenomic profiles analysis suggested that bacA may be the differential ARG subtype of two-stage AD process. ARG-like sequences encoding antibiotic efflux pump, antibiotic inactivation and antibiotic target alteration mechanisms were identified as the dominant ARGs resistance mechanisms in all samples. Procrustes analysis showed that microbial community composition structured the resistome. Co-occurrence patterns between ARGs and microbial phylogeny revealed that 26 bacterial species might be potential hosts of 94 ARG subtypes.},
}
@article {pmid33302073,
year = {2021},
author = {Li, M and Zhang, C},
title = {Are silver nanoparticles better than triclosan as a daily antimicrobial? Answers from the perspectives of gut microbiome disruption and pathogenicity.},
journal = {The Science of the total environment},
volume = {756},
number = {},
pages = {143983},
doi = {10.1016/j.scitotenv.2020.143983},
pmid = {33302073},
issn = {1879-1026},
mesh = {Anti-Bacterial Agents ; *Anti-Infective Agents ; *Gastrointestinal Microbiome ; Humans ; *Metal Nanoparticles/toxicity ; Silver/toxicity ; *Triclosan/toxicity ; Virulence ; },
abstract = {As an alternative to triclosan (TCS), the widespread use of silver nanoparticles (AgNPs) in daily products shows genuine potential. However, information regarding whether AgNPs are substantially better than TCS in their potential disruption of the gut microbiome and health effects is lacking. Using a simulator of the human intestinal microbial ecosystem (SHIME), we systemically compared the effects of TCS and AgNPs (at 1 μg/L and 30 μg/L) on the human gut microbiome in terms of changes in gut homeostasis, microbial community structure, antibiotic resistance profiles and abundances of opportunistic pathogens. Generally, TCS exerted more severe effects than AgNPs on gut disturbances (i.e., decreased production of short-chain fatty acids, increased contents of ammonium and total bile acids, and increased β-glucosidase activities) in a dose-dependent manner, whereas no clear dose effect was observed for the AgNP treatment because of potential nanoparticle transformation. The more serious effect of TCS than AgNPs on the microbiota composition was indicated by the dynamic increase in the Firmicutes/Bacteroidetes ratio determined using 16S rDNA sequencing. Metagenomic analyses revealed a more pronounced effect of TCS than AgNPs on the selection and dissemination of multiple resistance genes to antibiotics, TCS, and even Ag via the enrichment of genes encoding efflux pumps and mobile genetic elements. Consequently, the overgrowth of opportunistic pathogens was observed upon TCS exposure due to an imbalanced microbiome, in contrast to a slight increase in the abundance of some beneficial bacteria (i.e., Bifidobacterium) induced by the AgNP treatment. In conclusion, from the perspective of effects on gut health, AgNPs may prevail over TCS to some extent. However, the stress and potential selection of Ag resistance indicates the need for targeted surveillance of AgNP commercialization for daily use.},
}
@article {pmid33301716,
year = {2020},
author = {Wu, M and Kasper, DL},
title = {Fiber Sets up the Battleground for Intestinal Prevotella.},
journal = {Cell host &amp; microbe},
volume = {28},
number = {6},
pages = {776-777},
doi = {10.1016/j.chom.2020.11.010},
pmid = {33301716},
issn = {1934-6069},
abstract = {In this issue of Cell Host &amp; Microbe, Gálvez et al. employed metagenomic and phylogenetic analysis to systemically characterize murine Prevotella spp. Isolation of representative strains identified key fitness determinants, including arabinoxylan utilization loci, in a dominant murine colonizing strain and conserved in human gut microbiota, collectively facilitating the understanding of niches in the gut microbiota.},
}
@article {pmid33299088,
year = {2020},
author = {Malard, F and Dore, J and Gaugler, B and Mohty, M},
title = {Introduction to host microbiome symbiosis in health and disease.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
pmid = {33299088},
issn = {1935-3456},
abstract = {Humans share a core intestinal microbiome and yet human microbiome differs by genes, species, enterotypes (ecology), and gene count (microbial diversity). Achievement of microbiota metagenomic analysis has revealed that the microbiome gene count is a key stratifier of health in several immune disorders and clinical conditions. We review here the progress of the metagenomic pipeline analysis, and how this has allowed us to define the host-microbe symbiosis associated with a healthy status. The link between host-microbe symbiosis disruption, the so-called dysbiosis and chronic diseases or iatrogenic conditions is highlighted. Finally, opportunities to use microbiota modulation, with specific nutrients and/or live microbes, as a target for personalized nutrition and therapy for the maintenance, preservation, or restoration of host-microbe symbiosis are discussed.},
}
@article {pmid33299064,
year = {2020},
author = {Gusareva, ES and Gaultier, NPE and Premkrishnan, BNV and Kee, C and Lim, SBY and Heinle, CE and Purbojati, RW and Nee, AP and Lohar, SR and Yanqing, K and Kharkov, VN and Drautz-Moses, DI and Stepanov, VA and Schuster, SC},
title = {Taxonomic composition and seasonal dynamics of the air microbiome in West Siberia.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21515},
pmid = {33299064},
issn = {2045-2322},
abstract = {Here, we describe taxonomical composition, as well as seasonal and diel dynamics of airborne microbial communities in West Siberia. A total of 78 airborne biomass samples from 39 time intervals were analysed, within a temperature range of 48 °C (26 °C to - 22 °C). We observed a 5-170-fold decrease in DNA yield extracted from the airborne biomass in winter compared to summer, nevertheless, yielding sufficient material for metagenomic analysis. The airborne microbial communities included Actinobacteria and Proteobacteria, Ascomycota and Basidiomycota fungi as major components, as well as some Streptophyta plants. In summer, bacterial and fungal plant pathogens, and wood-rotting saprophytes were predominant. In winter, Ascomycota moulds and cold-related or stress environment bacterial species were enriched, while the fraction of wood-rotting and mushroom-forming Basidiomycota fungi was largely reduced. As recently reported for the tropical climate, the airborne microbial communities performed a diel cycle in summer, however, in winter diel dynamics were not observed.},
}
@article {pmid33299026,
year = {2020},
author = {Biagini, F and Calvigioni, M and Lapomarda, A and Vecchione, A and Magliaro, C and De Maria, C and Montemurro, F and Celandroni, F and Mazzantini, D and Mattioli-Belmonte, M and Ghelardi, E and Vozzi, G},
title = {A novel 3D in vitro model of the human gut microbiota.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21499},
pmid = {33299026},
issn = {2045-2322},
abstract = {Clinical trials and animal studies on the gut microbiota are often limited by the difficult access to the gut, restricted possibility of in vivo monitoring, and ethical issues. An easily accessible and monitorable in vitro model of the gut microbiota represents a valid tool for a wider comprehension of the mechanisms by which microbes interact with the host and with each other. Herein, we present a novel and reliable system for culturing the human gut microbiota in vitro. An electrospun gelatin structure was biofabricated as scaffold for microbial growth. The efficiency of this structure in supporting microbial proliferation and biofilm formation was initially assessed for five microbes commonly inhabiting the human gut. The human fecal microbiota was then cultured on the scaffolds and microbial biofilms monitored by confocal laser and scanning electron microscopy and quantified over time. Metagenomic analyses and Real-Time qPCRs were performed to evaluate the stability of the cultured microbiota in terms of qualitative and quantitative composition. Our results reveal the three-dimensionality of the scaffold-adhered microbial consortia that maintain the bacterial biodiversity and richness found in the original sample. These findings demonstrate the validity of the developed electrospun gelatin-based system for in vitro culturing the human gut microbiota.},
}
@article {pmid33298993,
year = {2020},
author = {Wong, MK and Nakao, M and Hyodo, S},
title = {Field application of an improved protocol for environmental DNA extraction, purification, and measurement using Sterivex filter.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21531},
pmid = {33298993},
issn = {2045-2322},
abstract = {Environmental DNA (eDNA) is increasingly popular as a useful non-invasive method to monitor and study biodiversity and community structure in freshwater and marine environments. To effectively extract eDNA from the filter surface is a fundamental factor determining the representativeness of the samples. We improved the eDNA extraction efficiency of an established Sterivex method by 12- to 16-fold using a larger volume of lysis buffer mix coupled with backflushing the cartridges. The DNeasy extraction column could be overloaded when the environmental sample input is high, possibly due to a higher nonspecific binding present in environmental samples, thus resulting in a relatively lower quantity measured. Therefore, we included an internal control DNA in the extraction to monitor the extraction and purification efficiencies in field samples, which is crucial for quantification of original eDNA concentration. The use of Takara Probe qPCR Mix supplemented with protein-based additives improved the robustness of the real time PCR assay on inhibitor-rich environmental samples, but prior purification by Qiagen PowerClean Pro Cleanup kit could be essential for inhibitor-rich water samples, even though the recovery rate was unexpectedly low (average 33.0%). The improved extraction and quantification complement the qualitative analyses including metabarcoding and metagenomics in field application.},
}
@article {pmid33298571,
year = {2020},
author = {Nunn, KL and Clair, GC and Adkins, JN and Engbrecht, K and Fillmore, T and Forney, LJ},
title = {Amylases in the Human Vagina.},
journal = {mSphere},
volume = {5},
number = {6},
pages = {},
pmid = {33298571},
issn = {2379-5042},
support = {P30 GM103324/GM/NIGMS NIH HHS/United States ; },
abstract = {Dominance of Lactobacillus species in vaginal communities is a hallmark of healthy conditions in the female genital tract. Key nutrients for lactobacilli include sugars produced when glycogen is degraded by α-amylase in the vagina. While α-amylase activity has been demonstrated in vaginal fluids, it is unclear whether α-amylases are produced solely by the host, bacteria in the vagina, or both. We screened cervicovaginal mucus from 23 reproductive-age women, characterized the species composition of vaginal communities, measured vaginal pH, and determined levels of amylase activity, glycogen, and lactic acid. Based on differences in these measured variables, one sample from each of four individual donors was selected for metagenomic and proteomic analyses. Of eight putative bacterial amylases identified in the assembled bacterial metagenomes, we detected four in vaginal fluids. These amylases were produced by various bacteria in different vaginal communities. Moreover, no two communities were the same in terms of which bacteria were producing amylases. Although we detected bacterial amylases in vaginal fluids, there was no clear association between the bacterial species that was dominant in a community and the level of amylase activity. This association was likely masked by the presence of human α-amylase, which was also detected in vaginal fluids. Finally, the levels of amylase activity and glycogen were only weakly associated. Our findings show, for the first time, that multiple amylases from both bacterial and human origins can be present simultaneously in the vagina. This work also suggests that the link between glycogen, amylase, and Lactobacillus in the vagina is complex.IMPORTANCE In this study, we show that multiple bacteria in the vaginal community produce amylases that hydrolyze glycogen into simpler sugars (i.e., maltose and maltotriose). These sugars serve as &quot;common goods&quot; that sustain bacterial populations in vaginal communities. Given the temporal changes that are observed in the human vaginal microbiome, we expect the kinds of bacterial amylases produced will also vary over time. These differences influence the pool of resources that are broadly shared and shape the species composition of the vaginal bacterial community.},
}
@article {pmid33297414,
year = {2020},
author = {Kyndt, JA and Van Beeumen, JJ and Meyer, TE},
title = {Simultaneous Genome Sequencing of Prosthecochloris ethylica and Desulfuromonasacetoxidans within a Syntrophic Mixture Reveals Unique Pili and Protein Interactions.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33297414},
issn = {2076-2607},
abstract = {Strains of Chloropseudomonas ethylica, 2-K, N2, and N3 are known to be composed of a syntrophic mixture of a green sulfur bacterium and a sulfur-reducing colorless component. Upon sequence analysis, the green sulfur photosynthetic bacterial component of strain N3 was dominant and was readily sequenced, but the less abundant sulfur-reducing bacterial component was apparent only when analyzed by metagenomic binning. Whole-genome comparison showed that the green bacterium belonged to the genus Prosthecochloris and apparently was a species for which there was no genome sequence on file. For comparison, we also sequenced the genome of Prosthecochloris sp. DSM 1685, which had previously been isolated from the 2-K mixture in pure culture and have shown that all three Prosthecochloris genomes belong to a new species, which we propose to be named Prosthecochloris ethylica comb. nov. Whole genomes were also sequenced for the isolated Desulfuromonas strains DSM 1675 (from strain 2-K) and DSM 1676 (from strain N2) and shown to be nearly identical to the genome found in the N3 mixture. The genome of the green sulfur bacterium contains large genes for agglutination proteins, similar to the ones proposed to be involved in larger photosynthetic consortia of Chlorochromatium aggregatum. In addition, we also identified several unique &quot;tight adhesion (tad)&quot; pili genes that are presumably involved in the formation of cell-cell interactions. The colorless component, on the other hand, contained a unique large multiheme cytochrome C and unique genes for e-pili (geopilin) formation, genetically clustered with a conserved ferredoxin gene, which are all expected to play an electron transfer role in the closed sulfur cycle in the syntrophic mixture. The findings from the simultaneous genome sequencing of the components of Cp. ethylica have implications for the phenomenon of direct interspecies interactions and coupled electron transfer in photosynthetic symbionts. The mechanisms for such interactions appear to be more common in the environment than originally anticipated.},
}
@article {pmid33297141,
year = {2021},
author = {Abdulsada, Z and Kibbee, R and Örmeci, B and DeRosa, M and Princz, J},
title = {Impact of anaerobically digested silver and copper oxide nanoparticles in biosolids on soil characteristics and bacterial community.},
journal = {Chemosphere},
volume = {263},
number = {},
pages = {128173},
doi = {10.1016/j.chemosphere.2020.128173},
pmid = {33297141},
issn = {1879-1298},
mesh = {Bacteria/genetics ; Biosolids ; Copper/toxicity ; *Metal Nanoparticles/toxicity ; Oxides ; RNA, Ribosomal, 16S ; Silver/analysis/toxicity ; Soil ; *Soil Pollutants/analysis/toxicity ; },
abstract = {This study investigated whether 2 and 30 mg AgNPs or CuONPs/g TS present in treated sludge (biosolids) may impact the soil health by monitoring the soil characteristics and soil bacterial community for 105 days after the application of biosolids. AgNPs or CuONPs/g TS were first anaerobically digested with mixed primary and secondary sludge rather than adding pristine nanoparticles to biosolids directly. Both environmentally relevant (under the USEPA ceiling concentration limits) and high concentrations of AgNPs and CuONPs were tested. Soil tests included TOC, TN, TP, pH, cell viability and heterotrophic plate counts (HPC). Metagenomic data was generated by high-throughput sequencing of the 16S rRNA gene to explore bacterial populations and diversity. AgNPs and CuONPs at 2 and 30 mg NPs/g TS of sludge could impact soil health factors such as bacterial diversity, community structure, and the population of plant growth-promoting rhizobacteria (PGPR). The population of the highly abundant bacteria that have important physiological roles in soil decreased, while the less important bacteria for soil function were able to thrive. CuONPs exhibited a higher level of toxicity than the AgNPs at both phylum and genus taxonomic levels, and the HPC decreased with higher concentrations of AgNPs and CuONPs. Initially, most of the studied phyla abundance was affected, but the control and other reactors approached similar levels by the end of the experiments, which may be explained by the decrease in toxicity due to the transformation of nanoparticles and the defence mechanisms of bacteria, and indicates the need for long-term field studies.},
}
@article {pmid33297037,
year = {2021},
author = {Chi, Y and Ren, T and Shi, X and Jin, X and Jin, P},
title = {Mechanism of nutrient removal enhancement in low carbon/nitrogen wastewater by a novel high-frequency micro-aeration/anoxic (HMOA) mode.},
journal = {Chemosphere},
volume = {263},
number = {},
pages = {128003},
doi = {10.1016/j.chemosphere.2020.128003},
pmid = {33297037},
issn = {1879-1298},
mesh = {Bioreactors ; Carbon ; *Nitrogen ; Nutrients ; Phosphorus ; Sewage ; Waste Disposal, Fluid ; *Waste Water ; },
abstract = {In this study, a novel high-frequency micro-aeration/anoxic (HMOA) mode with a high aeration frequency (15 times/h) and short aeration duration (Taer = 1 h/cycle) was proposed. Compared with continuous aeration modes, the highest nitrogen and phosphorus removal efficiencies were achieved in the sequencing batch reactor (SBR) under HMOA mode when treating wastewater with carbon/nitrogen (C/N) ratios of 4.5 (85% and 97%, respectively) and 3 (77% and 75%, respectively). Metagenomic analysis was utilized to analyse the microbial metabolic mechanism under the HMOA mode. The results showed that under the HMOA mode, the enhanced transduction and metabolism pathways of nitrate, nitrite, oxygen, phosphorus and acetate provided favourable nutritional conditions for the proliferation of denitrifiers and phosphorus accumulating organisms (PAOs), and simultaneously strengthened the survival capacity of nitrifiers under low dissolved oxygen (DO) conditions. In addition, genes involved in carbon metabolism were upregulated by the HMOA mode, which further increased the utility of carbon sources for denitrifier and PAO metabolism. Consequently, the limited carbon source could be fully utilized in nitrogen and phosphorus removal, which improved the efficiency of treating low C/N wastewater. This study proposed a potential aeration mode for microbial metabolism regulation to enhance nutrient removal in biological wastewater treatment processes.},
}
@article {pmid33296733,
year = {2020},
author = {Chen, H and Wang, Z and Liu, H and Nie, Y and Zhu, Y and Jia, Q and Ding, G and Ye, J},
title = {Variable sediment methane production in response to different source-associated sewer sediment types and hydrological patterns: Role of the sediment microbiome.},
journal = {Water research},
volume = {190},
number = {},
pages = {116670},
doi = {10.1016/j.watres.2020.116670},
pmid = {33296733},
issn = {1879-2448},
abstract = {Production of methane (CH4), an essential anthropogenic greenhouse gas, from municipal sewer sediment is a problem deserving intensive attention. Based on long-term laboratory batch tests in conjunction with 16 s rRNA gene sequencing and metagenomics, this study provides the first detailed assessment of the variable sediment CH4 production in response to different pollution source-associated sewer sediment types and hydrological patterns, while addressing the role of the sediment microbiome. The high CH4-production capability of sanitary sewer sediment is shaped by enriched biologically active substrate and dominated by acetoclastic methanogenesis (genus Methanosaeta). Moreover, it involves syntrophic interactions among fermentation bacteria, hydrogen-producing acetogens and methanogens. Distinct source-associated microbial species, denitrifying bacteria and sulfate-reducing bacteria occur in storm sewer and illicit discharge-associated (IDA) storm sewer sediments. This reveals their insufficient microbial function capabilities to support efficient methanogenesis. Hydrogenotrophic methanogenesis (genus Methanobacterium) prevails in both these sediments. In this context, storm sewer sediment has an extremely low CH4-production capability, while IDA storm sewer sediment still shows significant carbon emission through a possibly unique mechanism. Hydrological connections promote the sewer sediment biodegradability and CH4-production capability. In contrast, hydrological disconnection facilitates the prevalence of acetoclastic methanogenesis, sulfate-reducing enzymes, denitrification enzymes and the sulfur-utilizing chemolithoautotrophic denitrifier, which drastically decreases CH4 production. Turbulent suspension of sediments results in relative stagnation of methanogenesis. This work bridges the knowledge gap and will help to stimulate and guide the resolution of 'bottom-up' system-scale carbon budgets and GHG sources, as well as the target CH4 abatement interventions.},
}
@article {pmid33295091,
year = {2020},
author = {Hu, W and Pan, J and Wang, B and Guo, J and Li, M and Xu, M},
title = {Metagenomic insights into the metabolism and evolution of a new Thermoplasmata order (Candidatus Gimiplasmatales).},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15349},
pmid = {33295091},
issn = {1462-2920},
support = {2018GDASCX-0102//GDAS' Special Project of Science and Technology Development/ ; 2019GDASYL-0301002//GDAS' Special Project of Science and Technology Development/ ; 2021GDASYL-20210302001//GDAS' Special Project of Science and Technology Development/ ; 31970105//National Natural Science Foundation of China/ ; 51678163//National Natural Science Foundation of China/ ; 91851105//National Natural Science Foundation of China/ ; 91851202//National Natural Science Foundation of China/ ; 2018B020205003//The Key-Area Research and Development Program of Guangdong Province/ ; 2018B030324002//The Key-Area Research and Development Program of Guangdong Province/ ; 2019B110205004//The Key-Area Research and Development Program of Guangdong Province/ ; JCYJ20200109105010363//the Shenzhen Science and Technology Program/ ; },
abstract = {Thermoplasmata is a widely distributed and ecologically important archaeal class in the phylum Euryarchaeota. Because few cultures and genomes are available, uncharacterized Thermoplasmata metabolisms remain unexplored. In this study, we obtained four medium- to high-quality archaeal metagenome-assembled genomes (MAGs) from the filamentous fragments of black-odorous aquatic sediments (Foshan, Guangdong, China). Based on their 16S rRNA gene and ribosomal protein phylogenies, the four MAGs belong to the previously unnamed Thermoplasmata UBA10834 clade. We propose that this clade (five reference genomes from the Genome Taxonomy Database (GTDB) and four MAGs from this study) be considered a new order, Candidatus Gimiplasmatales. Metabolic pathway reconstructions indicated that the Ca. Gimiplasmatales MAGs can biosynthesize isoprenoids and nucleotides de novo. Additionally, some taxa have genes for formaldehyde and acetate assimilation, and the Wood-Ljungdahl CO2 -fixation pathway, indicating a mixotrophic lifestyle. Sulfur reduction, hydrogen metabolism, and arsenic detoxification pathways were predicted, indicating sulfur-, hydrogen-, and arsenic-transformation potentials. Comparative genomics indicated that the H4 F Wood-Ljungdahl pathway of both Ca. Gimiplasmatales and Methanomassiliicoccales was likely obtained by the interdomain lateral gene transfer from the Firmicutes. Collectively, this study elucidates the taxonomic and potential metabolic diversity of the new order Ca. Gimiplasmatales and the evolution of this subgroup and its sister lineage Methanomassiliicoccales.},
}
@article {pmid33295079,
year = {2020},
author = {Delgado Vela, J and Bristow, LA and Marchant, HK and Love, NG and Dick, GJ},
title = {Sulfide alters microbial functional potential in a methane and nitrogen cycling biofilm reactor.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15352},
pmid = {33295079},
issn = {1462-2920},
support = {//Burroughs Wellcome Fund/ ; EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; 1438560//Division of Chemical, Bioengineering, Environmental, and Transport Systems/ ; 695599//H2020 European Research Council/ ; ZN3184//Niedersächsisches Ministerium für Wissenschaft und Kultur/ ; //Max Planck Society/ ; //National Science Foundation Graduate Research Fellowship/ ; //Ford Foundation Dissertation Fellowship/ ; //University of Michigan Rackham Engineering Award/ ; },
abstract = {Cross-feeding of metabolites between coexisting cells leads to complex and interconnected elemental cycling and microbial interactions. These relationships influence overall community function and can be altered by changes in substrate availability. Here, we used isotopic rate measurements and metagenomic sequencing to study how cross-feeding relationships changed in response to stepwise increases of sulfide concentrations in a membrane-aerated biofilm reactor that was fed with methane and ammonium. Results showed that sulfide: (i) decreased nitrite oxidation rates but increased ammonia oxidation rates; (ii) changed the denitrifying community and increased nitrous oxide production; and (iii) induced dissimilatory nitrite reduction to ammonium (DNRA). We infer that inhibition of nitrite oxidation resulted in higher nitrite availability for DNRA, anammox, and nitrite-dependent anaerobic methane oxidation. In other words, sulfide likely disrupted microbial cross-feeding between AOB and NOB and induced cross-feeding between AOB and nitrite reducing organisms. Furthermore, these cross-feeding relationships were spatially distributed between biofilm and planktonic phases of the reactor. These results indicate that using sulfide as an electron donor will promote N2 O and ammonium production, which is generally not desirable in engineered systems.},
}
@article {pmid33294522,
year = {2020},
author = {Shaikhutdinov, N and Gogoleva, N and Gusev, O and Shagimardanova, E},
title = {Microbiota composition data of imago and larval stage of the anhydrobiotic midge.},
journal = {Data in brief},
volume = {33},
number = {},
pages = {106527},
pmid = {33294522},
issn = {2352-3409},
abstract = {The ability of larvae of a non-biting midge Polypedilum vanderplanki (Chironomidae) to withstand complete desiccation is a remarkable natural example of adaptation to extreme environment. In anhydrobiosis the larvae lose up to 99.2% of water and stay in a dry form until rainfall in natural environment or up to several decades in laboratory maintaining ability to restore activity soon after rehydration [1]. In the desiccated state, the larvae tolerate a variety of abiotic stresses, including high radiation exposure (7000Gry of 60Co gamma rays) [2]. Such a cross-resistance to desiccation and ionizing radiation is a characteristic of many anhydrobiotic organisms and believed to be based on similar molecular mechanisms. Microorganisms associated with the anhydrobiotic midge can also sustain desiccation and thus be radiation-resistant because desiccation-resistant prokaryotes are shown to be cross-resistant to ionizing radiation [3]. Microorganisms inhabiting larvae of the anhydrobiotic midge can also sustain desiccation and probably can sustain high doses of ionizing radiation. Therefore, it would be of interest to analyze the taxonomic and functional composition of microbiome of the anhydrobiotic midge. Sequencing data for the total DNA of anhydrobiotic organisms, which also contain reads derived from symbiotic microorganisms provide a promising opportunity to identify microorganisms with remarkable adaptation. It is known that at least some protective genes, such as late embryogenesis abundant (LEA) genes appeared in the genome of the midge by probable horizontal gene transfer from bacteria [1]. We performed shotgun sequencing of imago and larvae DNA samples using HiSeq 2000 and Genome Analyzer IIX System platforms. To assess microbiome diversity specific to anhydrobiotic midges, we analyzed Pool-seq data of the natural population of imago and Pool-seq data of final instar larvae. Data has been deposited in NCBI BioProject repository at NCBI under the accession number PRJNA659554 and consists of raw sequence data.},
}
@article {pmid33294140,
year = {2020},
author = {Babenko, VV and Millard, A and Kulikov, EE and Spasskaya, NN and Letarova, MA and Konanov, DN and Belalov, IS and Letarov, AV},
title = {The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {3457-3467},
pmid = {33294140},
issn = {2001-0370},
abstract = {The viromes of the mammalian lower gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing two groups of stabled horses, and a further group of feral horses that were isolated on an island. Our results indicate that the dsDNA viromes of the horse feces feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes, such as CrAssphage-related viruses found in humans, were identified. Additionally, many bacteriophage genus-level clusters were found to be present in all three geographically isolated populations. The diversity of the horse intestinal bacteriophages is severely undersampled, and so consequently only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways. Therefore, the diversity and structure of the intestinal virome in different animal species needs to be experimentally studied.},
}
@article {pmid33294135,
year = {2020},
author = {Tobias, NJ and Eberhard, FE and Guarneri, AA},
title = {Enzymatic biosynthesis of B-complex vitamins is supplied by diverse microbiota in the Rhodnius prolixus anterior midgut following Trypanosoma cruzi infection.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {3395-3401},
pmid = {33294135},
issn = {2001-0370},
abstract = {Trypanosoma cruzi, the causative agent of Chagas disease, colonizes the gut of triatomine insects, including Rhodnius prolixus. It is believed that this colonization upsets the microbiota that are normally present, presumably switching the environment to one more favorable for parasite survival. It was previously thought that one particular bacterium, Rhodococcus rhodnii, was essential for insect survival due to its ability to produce vital B-complex vitamins. However, these bacteria are not always identified in great abundance in studies on R. prolixus microbiota. Here we sequenced the microbiota of the insect anterior midgut using shotgun metagenomic sequencing in order to obtain a high-resolution snapshot of the microbes inside at two different time points and under two conditions; in the presence or absence of parasite and immediately following infection, or three days post-infection. We identify a total of 217 metagenomic bins, and recovered one metagenome-assembled genome, which we placed in the genus Dickeya. We show that, despite Rhodococcus being present, it is not the only microbe capable of synthesizing B-complex vitamins, with the genes required for biosynthesis present in a number of different microbes. This work helps to gain a new insight into the microbial ecology of R. prolixus.},
}
@article {pmid33293603,
year = {2020},
author = {Song, H and Kerfahi, D and Takahashi, K and Nixon, SL and Tripathi, BM and Kim, H and Tateno, R and Adams, J},
title = {Metagenomic analysis reveals rapid development of soil biota on fresh volcanic ash.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21419},
pmid = {33293603},
issn = {2045-2322},
abstract = {Little is known of the earliest stages of soil biota development of volcanic ash, and how rapidly it can proceed. We investigated the potential for soil biota development during the first 3 years, using outdoor mesocosms of sterile, freshly fallen volcanic ash from the Sakurajima volcano, Japan. Mesocosms were positioned in a range of climates across Japan and compared over 3 years, against the developed soils of surrounding natural ecosystems. DNA was extracted from mesocosms and community composition assessed using 16S rRNA gene sequences. Metagenome sequences were obtained using shotgun metagenome sequencing. While at 12 months there was insufficient DNA for sequencing, by 24 months and 36 months, the ash-soil metagenomes already showed a similar diversity of functional genes to the developed soils, with a similar range of functions. In a surprising contrast with our hypotheses, we found that the developing ash-soil community already showed a similar gene function diversity, phylum diversity and overall relative abundances of kingdoms of life when compared to developed forest soils. The ash mesocosms also did not show any increased relative abundance of genes associated with autotrophy (rbc, coxL), nor increased relative abundance of genes that are associated with acquisition of nutrients from abiotic sources (nifH). Although gene identities and taxonomic affinities in the developing ash-soils are to some extent distinct from the natural vegetation soils, it is surprising that so many of the key components of a soil community develop already by the 24-month stage. In this system, however, rapid development may be facilitated by the relatively moderate pH of the Sakurajima ash, proximity of our mesocosms to propagule sources, and the rapid establishment of a productive bryophyte and lichen layer on the surface. Ash from other volcanoes richer in acids or more distant from propagule sources could show a different pattern and slower soil biota development.},
}
@article {pmid33293569,
year = {2020},
author = {Faddetta, T and Ardizzone, F and Faillaci, F and Reina, C and Palazzotto, E and Strati, F and De Filippo, C and Spinelli, G and Puglia, AM and Gallo, G and Cavalieri, V},
title = {Composition and geographic variation of the bacterial microbiota associated with the coelomic fluid of the sea urchin Paracentrotus lividus.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21443},
pmid = {33293569},
issn = {2045-2322},
abstract = {In the present work, culture-based and culture-independent investigations were performed to determine the microbiota structure of the coelomic fluid of Mediterranean sea urchin Paracentrotus lividus individuals collected from two distinct geographical sites neighboring a high-density population bay and a nature reserve, respectively. Next Generation Sequencing analysis of 16S rRNA gene (rDNA) showed that members of the Proteobacteria, Bacteroidetes and Fusobacteria phyla, which have been previously reported to be commonly retrieved from marine invertebrates, dominate the overall population of microorganisms colonizing this liquid tissue, with minority bacterial genera exhibiting remarkable differences among individuals. Our results showed that there is a correlation between microbiota structure and geographical location of the echinoderm collection site, highlighting over-representation of metagenomic functions related to amino acid and bioactive peptides metabolism in specimens inhabiting the nature reserve. Finally, we also described the developmental delay and aberrations exhibited by sea urchin embryos exposed to distinct bacterial isolates, and showed that these defects rely upon hydrophilic compound(s) synthesized by the bacterial strains assayed. Altogether, our findings lay the groundwork to decipher the relationships of bacteria with sea urchins in their aquatic environment, also providing an additional layer of information to understand the biological roles of the coelomic fluid.},
}
@article {pmid33292949,
year = {2020},
author = {Song, D and Ho, CT and Zhang, X and Wu, Z and Cao, J},
title = {Modulatory effect of Cyclocarya paliurus flavonoids on the intestinal microbiota and liver clock genes of circadian rhythm disorder mice model.},
journal = {Food research international (Ottawa, Ont.)},
volume = {138},
number = {Pt A},
pages = {109769},
doi = {10.1016/j.foodres.2020.109769},
pmid = {33292949},
issn = {1873-7145},
abstract = {Host circadian rhythm and gut microbiota have a bidirectional relationship, indicating that prebiotics or prebiotic-like substance is a possible way to regulate circadian rhythm. The modulatory effect of Cyclocarya paliurus flavonoids (CPF) on the intestinal microbiota and liver clock genes of a circadian rhythm disorder mouse model was investigated in the present study. 16S rDNA sequencing analysis showed that CPF ameliorated the imbalanced intestinal microbial structure induced by circadian rhythm disorder. Compared with the constant darkness (CD) group, the ratio of the relative abundance of Firmicutes to Bacteroidetes was significantly decreased after the intervention of CPF for 4 weeks. In addition, CPF significantly alleviated the disrupted diurnal oscillation and phase shift of the specific intestinal microbes and liver clock genes induced by constant darkness. Moreover, metagenomics analysis of gut microbiota showed that the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched the most differentially expressed genes (DEGs) after CPF administration includes xenobiotics biodegradation and metabolism, carbohydrate metabolism and cell motility. The results suggested that CPF may positively regulate the gut flora disturbed by host circadian rhythm disorder, including its composition, diurnal oscillation and function, as well as affect the expression of liver clock genes, thus improving the host micro-ecology and health.},
}
@article {pmid33292445,
year = {2020},
author = {Tuveng, TR and Jensen, MS and Fredriksen, L and Vaaje-Kolstad, G and Eijsink, VGH and Forsberg, Z},
title = {A thermostable bacterial lytic polysaccharide monooxygenase with high operational stability in a wide temperature range.},
journal = {Biotechnology for biofuels},
volume = {13},
number = {1},
pages = {194},
pmid = {33292445},
issn = {1754-6834},
support = {221568//Norges Forskningsråd/ ; 268002//Norges Forskningsråd/ ; NNF18OC0055736//Novo Nordisk Fonden/ ; },
abstract = {BACKGROUND: Lytic polysaccharide monooxygenases (LPMOs) are oxidative, copper-dependent enzymes that function as powerful tools in the turnover of various biomasses, including lignocellulosic plant biomass. While LPMOs are considered to be of great importance for biorefineries, little is known about industrial relevant properties such as the ability to operate at high temperatures. Here, we describe a thermostable, cellulose-active LPMO from a high-temperature compost metagenome (called mgLPMO10).<br><br>RESULTS: MgLPMO10 was found to have the highest apparent melting temperature (83 °C) reported for an LPMO to date, and is catalytically active up to temperatures of at least 80 °C. Generally, mgLPMO10 showed good activity and operational stability over a wide temperature range. The LPMO boosted cellulose saccharification by recombinantly produced GH48 and GH6 cellobiohydrolases derived from the same metagenome, albeit to a minor extent. Cellulose saccharification studies with a commercial cellulase cocktail (Celluclast®) showed that the performance of this thermostable bacterial LPMO is comparable with that of a frequently utilized fungal LPMO from Thermoascus aurantiacus (TaLPMO9A).<br><br>CONCLUSIONS: The high activity and operational stability of mgLPMO10 are of both fundamental and applied interest. The ability of mgLPMO10 to perform oxidative cleavage of cellulose at 80 °C and the clear synergy with Celluclast® make this enzyme an interesting candidate in the development of thermostable enzyme cocktails for use in lignocellulosic biorefineries.},
}
@article {pmid33291533,
year = {2020},
author = {Aguayo, P and Campos, VL and Henríquez, C and Olivares, F and De Ia Iglesia, R and Ulloa, O and Vargas, CA},
title = {The Influence of pCO2-Driven Ocean Acidification on Open Ocean Bacterial Communities during A Short-Term Microcosm Experiment in the Eastern Tropical South Pacific (ETSP) off Northern Chile.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33291533},
issn = {2076-2607},
abstract = {Due to the increasing anthropogenic CO2 emissions, Ocean Acidification (OA) is progressing rapidly around the world. Despite the major role that microorganisms play on the marine biogeochemical cycling and ecosystem functioning, the response of bacterial communities upon OA scenarios is still not well understood. Here, we have conducted a detailed characterization of the composition and relative abundance of bacterial communities in the water column of an open-ocean station in the Eastern Tropical South Pacific (ETSP) off northern Chile and their interactions with environmental factors. In addition, through a short-term microcosm experiment, we have assessed the effect of low pH/high pCO2 conditions over the abundance and genetic diversity of bacterial communities. Our results evidence a clear partitioning of community composition that could be attributed mostly to dissolved oxygen. However, our experimental approach demonstrated that low pH/high pCO2 conditions might modify the structure of the bacterial community, evidencing that small changes in pH may impact significantly the abundance and diversity of key microorganisms. This study constitutes a first step aiming to provide insight about the influence of changing carbonate chemistry conditions on natural bacterial communities and to shed light on the potential impact of OA in biogeochemical cycles on the ETSP region.},
}
@article {pmid33291469,
year = {2020},
author = {Yang, C and Hu, H and Wu, Y and Lin, X and Fan, G and Duan, Y and Powell, C and Ancona, V and Zhang, M},
title = {Metagenomic Analysis Reveals the Mechanism for the Observed Increase in Antibacterial Activity of Penicillin against Uncultured Bacteria Candidatus Liberibacter asiaticus Relative to Oxytetracycline in Planta.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {9},
number = {12},
pages = {},
pmid = {33291469},
issn = {2079-6382},
support = {2018J05050//Natural Science Foundation of Fujian Province/ ; 2018R1013-6//Fujian Provincial Department of Science and Technology/ ; Guike AA 18118046//Science and Technology Major Project of Guangxi/ ; },
abstract = {Citrus huanglongbing (HLB) is a devastating disease for the citrus industry. The previous studies demonstrated that oxytetracycline and penicillin are effective antibiotics against Candidatus Liberibacter asiaticus (CLas). However, since CLas is uncultured, the mechanisms of action of antibiotics against CLas are still unclear. It was recently reported that the endophytic microbial communities are associated with the progression of citrus HLB after oxytetracycline and penicillin treatment. Therefore, we hypothesize that penicillin has greater antibacterial activity against CLas than oxytetracycline, which may be associated with the alteration of the structure and function of endophytic microbial communities in HLB-affected citrus in response to these antibiotics. To test this hypothesis, the microbiome of HLB-affected citrus leaves treated with these two antibiotics was analyzed using a metagenomic method. Our results indicate that the microbial structure and function in HLB-affected citrus were altered by these two antibiotics. The relative abundance of beneficial bacterial species, including Streptomyces avermitilis and Bradyrhizobium, was higher in penicillin-treated plants compared to those treated with oxytetracycline, and the relative abundance of the bacterial species (such as Propionibacterium acnes and Synechocystis sp PCC 6803) associated with CLas survival was lower for penicillin-treated plants compared to oxytetracycline-treated plants. These results indicate that penicillin has greater antibacterial activity against CLas. Based on the metagenomic analysis, this study elucidated the mechanism for the observed increase in antibacterial activity of penicillin against CLas. The data presented here are not only invaluable for developing eco-friendly and effective biocontrol strategies to combat citrus HLB, but also provide a method for revealing mechanism of antimicrobial against uncultured bacteria in host.},
}
@article {pmid33291220,
year = {2020},
author = {Hufsky, F and Beerenwinkel, N and Meyer, IM and Roux, S and Cook, GM and Kinsella, CM and Lamkiewicz, K and Marquet, M and Nieuwenhuijse, DF and Olendraite, I and Paraskevopoulou, S and Young, F and Dijkman, R and Ibrahim, B and Kelly, J and Le Mercier, P and Marz, M and Ramette, A and Thiel, V},
title = {The International Virus Bioinformatics Meeting 2020.},
journal = {Viruses},
volume = {12},
number = {12},
pages = {},
pmid = {33291220},
issn = {1999-4915},
mesh = {COVID-19 ; *Computational Biology ; Congresses as Topic ; Evolution, Molecular ; Genome, Viral ; Humans ; Metagenomics ; RNA Viruses/*genetics/pathogenicity ; *Virology ; },
abstract = {The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.},
}
@article {pmid33290743,
year = {2020},
author = {Chen, C and Li, J and Di, L and Jing, Q and Du, P and Song, C and Li, J and Li, Q and Cao, Y and Xie, XS and Wu, AR and Zeng, H and Huang, Y and Wang, J},
title = {MINERVA: A Facile Strategy for SARS-CoV-2 Whole-Genome Deep Sequencing of Clinical Samples.},
journal = {Molecular cell},
volume = {80},
number = {6},
pages = {1123-1134.e4},
doi = {10.1016/j.molcel.2020.11.030},
pmid = {33290743},
issn = {1097-4164},
abstract = {Analyzing the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from clinical samples is crucial for understanding viral spread and evolution as well as for vaccine development. Existing RNA sequencing methods are demanding on user technique and time and, thus, not ideal for time-sensitive clinical samples; these methods are also not optimized for high performance on viral genomes. We developed a facile, practical, and robust approach for metagenomic and deep viral sequencing from clinical samples. We demonstrate the utility of our approach on pharyngeal, sputum, and stool samples collected from coronavirus disease 2019 (COVID-19) patients, successfully obtaining whole metatranscriptomes and complete high-depth, high-coverage SARS-CoV-2 genomes with high yield and robustness. With a shortened hands-on time from sample to virus-enriched sequencing-ready library, this rapid, versatile, and clinic-friendly approach will facilitate molecular epidemiology studies during current and future outbreaks.},
}
@article {pmid33289802,
year = {2020},
author = {Haro-Moreno, JM and Coutinho, FH and Zaragoza-Solas, A and Picazo, A and Almagro-Moreno, S and López-Pérez, M},
title = {Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {12},
pages = {},
doi = {10.1093/femsec/fiaa218},
pmid = {33289802},
issn = {1574-6941},
abstract = {The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure, with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkably, below the cage the prokaryotic community was highly similar to the marine microbiome of photic offshore samples. We recovered 48 novel metagenome-assembled genomes. Metagenomic recruitment revealed a significant change in the microbial community which was dominated by several Proteobacteria orders (Sphingomonadales, Pseudomonadales, Caudobacterales and Rhizobiales). Genomic potential for bioremediation processes, including nitrate removal through aerobic denitrification, and degradation of aromatic compounds and other toxic products were enriched in these microbes. The detrimental side effects were the increased number of antimicrobial resistance genes and the presence of potentially emergent pathogens. Knowledge of this metabolic diversity and the microbes involved in ecological balance recovery can be used to reduce the environmental impact of these practices.},
}
@article {pmid33288859,
year = {2020},
author = {Pereira, O and Hochart, C and Boeuf, D and Auguet, JC and Debroas, D and Galand, PE},
title = {Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes (Ca. Poseidoniales) in the North Western Mediterranean Sea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-020-00851-4},
pmid = {33288859},
issn = {1751-7370},
support = {ANR-14-CE02-0004-01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {The Archaea Marine Group II (MGII) is widespread in the world's ocean where it plays an important role in the carbon cycle. Despite recent discoveries on the group's metabolisms, the ecology of this newly proposed order (Candidatus Poseidoniales) remains poorly understood. Here we used a combination of time-series metagenome-assembled genomes (MAGs) and high-frequency 16S rRNA data from the NW Mediterranean Sea to test if the taxonomic diversity within the MGIIb family (Candidatus Thalassarchaeaceae) reflects the presence of different ecotypes. The MAGs' seasonality revealed a MGIIb family composed of different subclades that have distinct lifestyles and physiologies. The vitamin metabolisms were notably different between ecotypes with, in some, a possible link to sunlight's energy. Diverse archaeal proteorhodopsin variants, with unusual signature in key amino acid residues, had distinct seasonal patterns corresponding to changing day length. In addition, we show that in summer, archaea, as opposed to bacteria, disappeared completely from surface waters. Our results shed light on the diversity and the distribution of the euryarchaeotal proteorhodopsin, and highlight that MGIIb is a diverse ecological group. The work shows that time-series based studies of the taxonomy, seasonality, and metabolisms of marine prokaryotes is critical to uncover their diverse role in the ocean.},
}
@article {pmid33288384,
year = {2020},
author = {Pallen, MJ and Telatin, A and Oren, A},
title = {The Next Million Names for Archaea and Bacteria.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2020.10.009},
pmid = {33288384},
issn = {1878-4380},
abstract = {Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains difficult and slow and typically relies on expert-driven nomenclatural quality control. Keen to ensure that the legacy of Linnaeus lives on in the age of microbial genomics and metagenomics, we propose an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed. As proof of principle, we document over a million new names for Bacteria and Archaea. We are confident that our approach provides a road map for how to create new names for decades to come.},
}
@article {pmid33287416,
year = {2020},
author = {Averina, OV and Zorkina, YA and Yunes, RA and Kovtun, AS and Ushakova, VM and Morozova, AY and Kostyuk, GP and Danilenko, VN and Chekhonin, VP},
title = {Bacterial Metabolites of Human Gut Microbiota Correlating with Depression.},
journal = {International journal of molecular sciences},
volume = {21},
number = {23},
pages = {},
pmid = {33287416},
issn = {1422-0067},
support = {20-14-00132//Russian Science Foundation/ ; },
abstract = {Depression is a global threat to mental health that affects around 264 million people worldwide. Despite the considerable evolution in our understanding of the pathophysiology of depression, no reliable biomarkers that have contributed to objective diagnoses and clinical therapy currently exist. The discovery of the microbiota-gut-brain axis induced scientists to study the role of gut microbiota (GM) in the pathogenesis of depression. Over the last decade, many of studies were conducted in this field. The productions of metabolites and compounds with neuroactive and immunomodulatory properties among mechanisms such as the mediating effects of the GM on the brain, have been identified. This comprehensive review was focused on low molecular weight compounds implicated in depression as potential products of the GM. The other possible mechanisms of GM involvement in depression were presented, as well as changes in the composition of the microbiota of patients with depression. In conclusion, the therapeutic potential of functional foods and psychobiotics in relieving depression were considered. The described biomarkers associated with GM could potentially enhance the diagnostic criteria for depressive disorders in clinical practice and represent a potential future diagnostic tool based on metagenomic technologies for assessing the development of depressive disorders.},
}
@article {pmid33285231,
year = {2020},
author = {Zhao, X and Oduro, PK and Tong, W and Wang, Y and Gao, X and Wang, Q},
title = {Therapeutic potential of natural products against atherosclerosis: Targeting on gut microbiota.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {105362},
doi = {10.1016/j.phrs.2020.105362},
pmid = {33285231},
issn = {1096-1186},
abstract = {Gut microbiota (GM) has emerged as an essential and integral factor for maintaining human health and affecting pathological outcomes. Metagenomics and metabolomics characterization have furthered gut metagenome's understanding and unveiled that deviation of specific GM community members and GM-dependent metabolites imbalance orchestrate metabolic or cardiovascular diseases (CVDs). Restoring GM ecosystem with nutraceutical supplements keenly prebiotics and probiotics relatively decreases CVDs incidence and overall mortality. In Atherosclerosis, commensal and pathogenic gut microbes correlate with atherogenesis events. GM-dependent metabolites-trimethylamine N-oxide and short-chain fatty acids regulate atherosclerosis-related metabolic processes in opposite patterns to affect atherosclerosis outcomes. Therefore, GM might be a potential therapeutic target for atherosclerosis. In atherogenic animal models, natural products with cardioprotective properties could modulate the GM ecosystem by revitalizing healthier GM phylotypes and abrogating proatherogenic metabolites, paving future research paths for clinical therapeutics.},
}
@article {pmid33283181,
year = {2020},
author = {Souza, TML and Morel, CM},
title = {The COVID-19 pandemics and the relevance of biosafety facilities for metagenomics surveillance, structured disease prevention and control.},
journal = {Biosafety and health},
volume = {},
number = {},
pages = {},
pmid = {33283181},
issn = {2590-0536},
abstract = {The 2019 coronavirus disease (COVID-19) pandemic represents an enormous challenge to all countries, regardless of their development status. The manipulation of its etiologic agent SARS-CoV-2 requires a biosafety containment level 3 laboratories (BSL-3) to understand virus biology and in vivo pathogenesis as well as the translation of new knowledge into the preclinical development of vaccines and antivirals. As such, BSL-3 facilities should be considered an integral part of any public health response to emerging infectious disease prevention, control and management. Differently from BSL2, BSL-3 units vary considerably along the range from industrialized to the least developed countries. Innovative Developing Countries (IDCs) such as Brazil, which excelled at controlling the 2015-2017 Zika epidemic, had to face a serious flaw in its disease control and prevention structure: the scarcity and uneven geographic distribution of its BSL-3 facilities, including those for preclinical animal experimentation.},
}
@article {pmid33282748,
year = {2020},
author = {Nath, S and Kumari, N and Bandyopadhyay, D and Sinha, N and Majumder, PP and Mitra, R and Mukherjee, S},
title = {Dysbiotic Lesional Microbiome With Filaggrin Missense Variants Associate With Atopic Dermatitis in India.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {570423},
pmid = {33282748},
issn = {2235-2988},
abstract = {Background: Atopic Dermatitis (AD) has been associated with the loss of function (LoF) mutations in Filaggrin (FLG) gene and increase in relative abundance of specific microbes in the lesional skin, predominantly in Caucasians. Our study aims to determine, in Indian AD patients, (a) the prevalence of FLG LoF and missense mutations, and (b) the nature and extent of dysbiosis and altered microbial pathways with and without mutations in FLG. AD patients (n = 34) and healthy controls (n = 54) were recruited from India in this study and shotgun sequencing was carried out in a subset of samples with adequate microbiome DNA concentration. Host DNA from the same subset of samples was subjected to FLG coding region sequencing and host-microbiome association was estimated. Results: The prevalence of FLG LoFs that are associated with AD globally were significantly lesser in our cases and controls (8.6%, 0%) than those reported in Europeans (27%, 2.6%). Staphylococcus aureus was present only on AD skin [abundance in Pediatric AD: 32.86%; Adult AD: 22.17%], but not on healthy skin on which Staphylococcus hominis (Adult controls: 16.43%, Adult AD: 0.20%; p = 0.002), Cutibacterium acnes (Adult controls:10.84%, Adult AD: 0.90%; p = 0.02), and Malassezia globosa (Adult controls: 8.89%, Adult AD: 0.005%; p = 0.001) were significantly more abundant. Microbial pathways mostly associated with skin barrier permeability, ammonia production and inflammation (Arginine and Proline metabolism, Histidine Metabolism and Staphylococcus aureus infection) were significantly enriched on AD skin metagenome. These pathways are also reported to impair antimicrobial peptide activity. Among AD patients with missense single nucleotide polymorphisms harboring &quot;potentially damaging&quot; alleles in FLG gene, damaging allele dosage was significantly (p < 0.02) positively correlated with relative abundance of phylum_Proteobacteria up to order_Pseudomonadales and negatively correlated with phylum_Firmicutes up to species_Staphylococcus aureus. Conclusion: Our study has provided evidence that host DNA profile is significantly associated with microbiome composition in the development of AD. Species and strain level analysis showed that the microbial pathways enriched in AD cases were mostly found in MRSA strains. These evidences can be harnessed to control AD by modulating the microbiome using a personalized strategy. Our findings on the association of FLG genotypes with the microbiome dysbiosis may pave the way for a personalized strategy to provide a more effective control of AD.},
}
@article {pmid33281861,
year = {2020},
author = {, },
title = {Erratum: From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {614083},
doi = {10.3389/fpls.2020.614083},
pmid = {33281861},
issn = {1664-462X},
abstract = {[This corrects the article DOI: 10.3389/fpls.2020.01179.].},
}
@article {pmid33281796,
year = {2020},
author = {Broddrick, JT and Szubin, R and Norsigian, CJ and Monk, JM and Palsson, BO and Parenteau, MN},
title = {High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {596626},
pmid = {33281796},
issn = {1664-302X},
support = {U01 AI124316/AI/NIAID NIH HHS/United States ; },
abstract = {Advances in nanopore-based sequencing techniques have enabled rapid characterization of genomes and transcriptomes. An emerging application of this sequencing technology is point-of-care characterization of pathogenic bacteria. However, genome assessments alone are unable to provide a complete understanding of the pathogenic phenotype. Genome-scale metabolic reconstruction and analysis is a bottom-up Systems Biology technique that has elucidated the phenotypic nuances of antimicrobial resistant (AMR) bacteria and other human pathogens. Combining these genome-scale models (GEMs) with point-of-care nanopore sequencing is a promising strategy for combating the emerging health challenge of AMR pathogens. However, the sequencing errors inherent to the nanopore technique may negatively affect the quality, and therefore the utility, of GEMs reconstructed from nanopore assemblies. Here we describe and validate a workflow for rapid construction of GEMs from nanopore (MinION) derived assemblies. Benchmarking the pipeline against a high-quality reference GEM of Escherichia coli K-12 resulted in nanopore-derived models that were >99% complete even at sequencing depths of less than 10× coverage. Applying the pipeline to clinical isolates of pathogenic bacteria resulted in strain-specific GEMs that identified canonical AMR genome content and enabled simulations of strain-specific microbial growth. Additionally, we show that treating the sequencing run as a mock metagenome did not degrade the quality of models derived from metagenome assemblies. Taken together, this study demonstrates that combining nanopore sequencing with GEM construction pipelines enables rapid, in situ characterization of microbial metabolism.},
}
@article {pmid33281778,
year = {2020},
author = {Palmer, M and Hedlund, BP and Roux, S and Tsourkas, PK and Doss, RK and Stamereilers, C and Mehta, A and Dodsworth, JA and Lodes, M and Monsma, S and Glavina Del Rio, T and Schoenfeld, TW and Eloe-Fadrosh, EA and Mead, DA},
title = {Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {583361},
pmid = {33281778},
issn = {1664-302X},
abstract = {Despite the high abundance of Aquificae in many geothermal systems, these bacteria are difficult to culture and no viruses infecting members of this phylum have been isolated. Here, we describe the complete, circular dsDNA Uncultivated Virus Genome (UViG) of Thermocrinis Octopus Spring virus (TOSV), derived from metagenomic data, along with eight related UViGs representing three additional viral species. Despite low overall similarity among viruses from different hot springs, the genomes shared a high degree of synteny, and encoded numerous genes for nucleotide metabolism, including a PolA-type DNA polymerase polyprotein with likely accessory functions, a DNA Pol III sliding clamp, a thymidylate kinase, a DNA gyrase, a helicase, and a DNA methylase. Also present were conserved genes predicted to code for phage capsid, large and small subunits of terminase, portal protein, holin, and lytic transglycosylase, all consistent with a distant relatedness to cultivated Caudovirales. These viruses are predicted to infect Aquificae, as multiple CRISPR spacers matching the viral genomes were identified within the genomes and metagenomic contigs from these bacteria. Based on the predicted atypical bi-directional replication strategy, low sequence similarity to known viral genomes, and unique position in gene-sharing networks, we propose a new putative genus, &quot;Pyrovirus,&quot; in the order Caudovirales.},
}
@article {pmid33281771,
year = {2020},
author = {Lafond, M and Tauzin, AS and Bruel, L and Laville, E and Lombard, V and Esque, J and André, I and Vidal, N and Pompeo, F and Quinson, N and Perrier, J and Fons, M and Potocki-Veronese, G and Giardina, T},
title = {α-Galactosidase and Sucrose-Kinase Relationships in a Bi-functional AgaSK Enzyme Produced by the Human Gut Symbiont Ruminococcus gnavus E1.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {579521},
pmid = {33281771},
issn = {1664-302X},
abstract = {Plant α-galactosides belonging to the raffinose family oligosaccharides (RFOs) and considered as prebiotics, are commonly degraded by α-galactosidases produced by the human gut microbiome. In this environment, the Ruminococcus gnavus E1 symbiont-well-known for various benefit-is able to produce an original RgAgaSK bifunctional enzyme. This enzyme contains an hydrolytic α-galactosidase domain linked to an ATP dependent extra-domain, specifically involved in the α-galactoside hydrolysis and the phosphorylation of the glucose, respectively. However, the multi-modular relationships between both catalytic domains remained hitherto unexplored and has been, consequently, herein investigated. Biochemical characterization of heterologously expressed enzymes either in full-form or in separated domains revealed similar kinetic parameters. These results were supported by molecular modeling studies performed on the whole enzyme in complex with different RFOs. Further enzymatic analysis associated with kinetic degradation of various substrates followed by high pressure anionic exchange chromatography revealed that catalytic efficiency decreased as the number of D-galactosyl moieties branched onto the oligosaccharide increased, suggesting a preference of RgAgaSK for RFO's short chains. A wide prevalence and abundance study on a human metagenomic library showed a high prevalence of the RgAgaSK encoding gene whatever the health status of the individuals. Finally, phylogeny and synteny studies suggested a limited spread by horizontal transfer of the clusters' containing RgAgaSK to only few species of Firmicutes, highlighting the importance of these undispersed tandem activities in the human gut microbiome.},
}
@article {pmid33281767,
year = {2020},
author = {Wang, R and Ding, W and Long, L and Lan, Y and Tong, H and Saha, S and Wong, YH and Sun, J and Li, Y and Zhang, W and Qian, PY},
title = {Exploring the Influence of Signal Molecules on Marine Biofilms Development.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {571400},
pmid = {33281767},
issn = {1664-302X},
abstract = {Microbes respond to environmental stimuli through complicated signal transduction systems. In microbial biofilms, because of complex multiple species interactions, signals transduction systems are of an even higher complexity. Here, we performed a signal-molecule-treatment experiment to study the role of different signal molecules, including N-hexanoyl-L-homoserine lactone (C6-HSL), N-dodecanoyl-L-homoserine lactone (C12-HSL), Pseudomonas quinolone signal (PQS), and cyclic di-GMP (c-di-GMP), in the development of marine biofilms. Comparative metagenomics suggested a distinctive influence of these molecules on the microbial structure and function of multi-species biofilm communities in its developing stage. The PQS-treated biofilms shared the least similarity with the control and initial biofilms. The role of PQS in biofilm development was further explored experimentally with the strain Erythrobacter sp. HKB8 isolated from marine biofilms. Comparative transcriptomic analysis showed that 314 genes, such as those related to signal transduction and biofilm formation, were differentially expressed in the untreated and PQS-treated Erythrobacter sp. HKB8 biofilms. Our study demonstrated the different roles of signal molecules in marine biofilm development. In particular, the PQS-based signal transduction system, which is frequently detected in marine biofilms, may play an important role in regulating microbe-microbe interactions and the assemblage of biofilm communities.},
}
@article {pmid33281758,
year = {2020},
author = {Jansen, SA and Nijhuis, W and Leavis, HL and Riezebos-Brilman, A and Lindemans, CA and Schuurman, R},
title = {Broad Virus Detection and Variant Discovery in Fecal Samples of Hematopoietic Transplant Recipients Using Targeted Sequence Capture Metagenomics.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {560179},
pmid = {33281758},
issn = {1664-302X},
abstract = {Pediatric allogeneic hematopoietic stem cell transplantation (HSCT) patients often suffer from gastro-intestinal (GI) disease caused by viruses, Graft-versus-Host Disease (GVHD) or a combination of the two. Currently, the GI eukaryotic virome of HSCT recipients remains relatively understudied, which complicates the understanding of its role in GVHD pathogenicity. As decisions regarding immunosuppressive therapy in the treatment of virus infection or GVHD, respectively, can be completely contradicting, it is crucial to better understand the prevalence and relevance of viruses in the GI tract in the HSCT setting. A real time PCR panel for a set of specific viruses widely used to diagnose the most common causes of GI viral gastroenteritis is possibly insufficient to grasp the full extent of viruses present. Therefore, we applied the targeted sequence capture method ViroCap to residual fecal samples of 11 pediatric allogeneic HSCT recipients with GI symptoms and a suspicion of GVHD, to enrich for nucleic acids of viruses that are known to infect vertebrate hosts. After enrichment, NGS was applied to broadly detect viral sequences. Using ViroCap, we were able to detect viruses such as norovirus and adenovirus (ADV), that had been previously detected using clinical diagnostic PCR on the same sample. In addition, multiple, some of which clinically relevant viruses were detected, including ADV, human rhinovirus (HRV) and BK polyomavirus (BKV). Interestingly, in samples in which specific PCR testing for regular viral GI pathogens did not result in a diagnosis, the ViroCap pipeline led to the detection of viral sequences of human herpesvirus (HHV)-7, BKV, HRV, KI polyomavirus and astrovirus. The latter was an only recently described variant and showed extensive sequence mismatches with the applied real time PCR primers and would therefore not have been detected if tested. Our results indicate that target enrichment of viral nucleic acids through ViroCap leads to sensitive and broad possibly clinically relevant virus detection, including the detection of newer variants in clinical HSCT recipient samples. As such, ViroCap could be a useful detection tool clinically, but also in studying the associations between viral presence and GVHD.},
}
@article {pmid33281440,
year = {2020},
author = {Joseph, N and Clayton, JB and Hoops, SL and Linhardt, CA and Mohd Hashim, A and Mohd Yusof, BN and Kumar, S and Amin Nordin, S},
title = {Alteration of the Gut Microbiome in Normal and Overweight School Children from Selangor with Lactobacillus Fermented Milk Administration.},
journal = {Evolutionary bioinformatics online},
volume = {16},
number = {},
pages = {1176934320965943},
pmid = {33281440},
issn = {1176-9343},
abstract = {Childhood obesity is a serious public health problem worldwide. Perturbations in the gut microbiota composition have been associated with the development of obesity in both children and adults. Probiotics, on the other hand, are proven to restore the composition of the gut microbiome which helps reduce the development of obesity. However, data on the effect of probiotics on gut microbiota and its association with childhood obesity is limited. This study aims to determine the effect of probiotics supplement intervention on gut microbiota profiles in obese and normal-weight children. A total of 37 children, 17 normal weight, and 20 overweight school children from a government school in Selangor were selected to participate in this study. Participants were further divided into intervention and control groups. The intervention groups received daily probiotic drinks while the control groups continued eating their typical diet. Fecal samples were collected from the participants for DNA extraction. The hypervariable V3 and V4 regions of 16S rRNA gene were amplified and sequenced using the Illumina MiSeq platform. No significant differences in alpha diversity were observed between normal weight and obese children in terms of the Shannon Index for evenness or species richness. However, a higher intervention effect on alpha diversity was observed among normal-weight participants compared to obese. The participants' microbiome was found to fluctuate throughout the study. Analysis of the taxa at species level showed an increase in Bacteroides ovatus among the normal weight cohort. Genus-level comparison revealed a rise in genus Lachnospira and Ruminococcus in the overweight participants after intervention, compared to the normal-weight participants. The probiotics intervention causes an alteration in gut microbiota composition in both normal and overweight children. Though the association could not be defined statistically, this study has provided an improved understanding of the intervention effect of probiotics on gut microbiome dysbiosis in an underrepresented population.},
}
@article {pmid33281127,
year = {2020},
author = {Nakajima, Y and Kojima, K and Kashiyama, Y and Doi, S and Nakai, R and Sudo, Y and Kogure, K and Yoshizawa, S},
title = {Bacterium Lacking a Known Gene for Retinal Biosynthesis Constructs Functional Rhodopsins.},
journal = {Microbes and environments},
volume = {35},
number = {4},
pages = {},
pmid = {33281127},
issn = {1347-4405},
abstract = {Microbial rhodopsins, comprising a protein moiety (rhodopsin apoprotein) bound to the light-absorbing chromophore retinal, function as ion pumps, ion channels, or light sensors. However, recent genomic and metagenomic surveys showed that some rhodopsin-possessing prokaryotes lack the known genes for retinal biosynthesis. Since rhodopsin apoproteins cannot absorb light energy, rhodopsins produced by prokaryotic strains lacking genes for retinal biosynthesis are hypothesized to be non-functional in cells. In the present study, we investigated whether Aurantimicrobium minutum KNCT, which is widely distributed in terrestrial environments and lacks any previously identified retinal biosynthesis genes, possesses functional rhodopsin. We initially measured ion transport activity in cultured cells. A light-induced pH change in a cell suspension of rhodopsin-possessing bacteria was detected in the absence of exogenous retinal. Furthermore, spectroscopic analyses of the cell lysate and HPLC-MS/MS analyses revealed that this strain contained an endogenous retinal. These results confirmed that A. minutum KNCT possesses functional rhodopsin and, hence, produces retinal via an unknown biosynthetic pathway. These results suggest that rhodopsin-possessing prokaryotes lacking known retinal biosynthesis genes also have functional rhodopsins.},
}
@article {pmid33280938,
year = {2020},
author = {Sharma, M and Khurana, H and Singh, DN and Negi, RK},
title = {The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review.},
journal = {Journal of environmental management},
volume = {},
number = {},
pages = {111744},
doi = {10.1016/j.jenvman.2020.111744},
pmid = {33280938},
issn = {1095-8630},
abstract = {The genus Sphingopyxis was first reported in the year 2001. Phylogenetically, Sphingopyxis is well delineated from other genera Sphingobium, Sphingomonas and Novosphingobium of sphingomonads group, family Sphingomonadaceae of Proteobacteria. To date (at the time of writing), the genus Sphingopyxis comprises of twenty validly published species available in List of Prokaryotic Names with Standing in Nomenclature. Sphingopyxis spp. have been isolated from diverse niches including, agricultural soil, marine and fresh water, caves, activated sludge, thermal spring, oil and pesticide contaminated soil, and heavy metal contaminated sites. Sphingopyxis species have drawn considerable attention not only for their ability to survive under extreme environments, but also for their potential to degrade number of xenobiotics and other environmental contaminants that impose serious threat to human health. At present, genome sequence of both cultivable and non-cultivable strains (metagenome assembled genome) are available in the public databases (NCBI) and genome wide studies confirms the presence of mobile genetic elements and plethora of degradation genes and pathways making them a potential candidate for bioremediation. Beside genome wide predictions there are number of experimental evidences confirm the degradation potential of bacteria belonging to genus Sphingopyxis and also the production of different secondary metabolites that help them interact and survive in their ecological niches. This review provides detailed information on ecology, general characteristic and the significant implications of Sphingopyxis species in environmental management along with the bio-synthetic potential.},
}
@article {pmid33278791,
year = {2020},
author = {López-Labrador, FX and Brown, JR and Fischer, N and Harvala, H and Van Boheemen, S and Cinek, O and Sayiner, A and Madsen, TV and Auvinen, E and Kufner, V and Huber, M and Rodriguez, C and Jonges, M and Hönemann, M and Susi, P and Sousa, H and Klapper, PE and Pérez-Cataluňa, A and Hernandez, M and Molenkamp, R and der Hoek, LV and Schuurman, R and Couto, N and Leuzinger, K and Simmonds, P and Beer, M and Höper, D and Kamminga, S and Feltkamp, MCW and Rodríguez-Díaz, J and Keyaerts, E and Nielsen, XC and Puchhammer-Stöckl, E and Kroes, ACM and Buesa, J and Breuer, J and Claas, ECJ and de Vries, JJC and , },
title = {Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {134},
number = {},
pages = {104691},
doi = {10.1016/j.jcv.2020.104691},
pmid = {33278791},
issn = {1873-5967},
abstract = {Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.},
}
@article {pmid33278636,
year = {2020},
author = {Phan, T and Ide, T and Komoto, S and Khamrin, P and Pham, NTK and Okitsu, S and Taniguchi, K and Nishimura, S and Maneekarn, N and Hayakawa, S and Ushijima, H},
title = {Genomic analysis of group A rotavirus G12P[8] including a new Japanese strain revealed evidence for intergenotypic recombination in VP7 and VP4 genes.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {87},
number = {},
pages = {104656},
doi = {10.1016/j.meegid.2020.104656},
pmid = {33278636},
issn = {1567-7257},
abstract = {Group A rotavirus is a leading cause of severe acute gastroenteritis worldwide. In this study, the first complete coding sequences of 11 RNA segments of human group A rotavirus G12P[8] in Japan were determined by an unbiased viral metagenomics. Its genomic constellation (VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes) was identified as G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. When performing the genetic analysis, we discovered an intergenotypic recombination event in the pig group A rotavirus G12P[8] strain BUW-14-A008. The novel recombination was found between two different genotypes G12 and G3 in the VP7 gene, and P[8] and P[13] in the VP4 gene.},
}
@article {pmid33278555,
year = {2020},
author = {Reyes, AC and Egwu, E and Yu, E and Sanchez, AN and De La O, L and Elijah, OE and Muschalek, TJ and Zhang, W and Ji, H and Ehsan, H and Kaneko, G},
title = {Forkhead transcription factor O1 (FoxO1) in torafugu pufferfish Takifugu rubripes: Molecular cloning, in vitro DNA binding, and target gene screening in fish metagenome.},
journal = {Gene},
volume = {768},
number = {},
pages = {145335},
doi = {10.1016/j.gene.2020.145335},
pmid = {33278555},
issn = {1879-0038},
abstract = {The fish insulin/insulin-like growth factor (IGF) pathway has weak control over carbohydrate metabolism. To understand the molecular basis for the metabolic diversity, we characterized the forkhead box transcription factor O1A (FoxO1A), a downstream target of the insulin/IGF pathway, in torafugu Takifugu rubripes. The cloned torafugu FoxO1A cDNA contained all conserved features critical for its transcriptional activity and a unique unspliced intron encoding a poly-glutamine stretch. Torafugu FoxO1A showed the IGF-dependent nuclear exclusion and in vitro binding to the well-conserved FoxO1 binding site, DAF-16 binding element (DBE), but failed to bind to the insulin-responsive element by which mammalian FoxO1 mediates insulin effects. The subsequent in silico genomic screening provided a list of 587 potential torafugu FoxO1A target genes containing the DBE. Some carbohydrate metabolic genes regulated by FoxO1 in mammals were not included in the list. We further identified about 250 potential fish FoxO1 target genes by integrating results of the DBE screening against fish metagenome that contained 262 species. Neuronal processes appeared to be the common major function of fish FoxO1, although further annotation of the potential target genes is required. These results provide a part of the molecular basis underlying the weak association between the insulin/IGF pathway and carbohydrate metabolism in fish.},
}
@article {pmid33278015,
year = {2020},
author = {Jia, S and Li, T and Zhang, XX},
title = {Integrated metagenomic and metatranscriptomic analyses of ultraviolet disinfection effects on antibiotic resistance genes and bacterial communities during wastewater treatment.},
journal = {Ecotoxicology (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10646-020-02313-1},
pmid = {33278015},
issn = {1573-3017},
support = {ZYJH005//Nanjing University Excellent Research Program/ ; 51908274//Young Scientists Fund/ ; 2018M640475//Postdoctoral Research Foundation of China/ ; },
abstract = {Ultraviolet (UV) disinfection is now widely implemented in wastewater treatment plants (WWTPs) worldwide, but its effect on antibiotic resistome of the surviving bacteria remains unclear. In this study, we employed high-throughput sequencing-based metagenomic and metatranscriptomic approaches to comprehensively elucidate the effects of UV disinfection on the shifts of bacterial community and antibiotic resistance genes (ARGs) on both DNA and mRNA levels in one WWTP. Metagenomic analyses revealed an insignificant change in the bacterial community after UV disinfection, while metatranscriptomic analyses showed that UV disinfection significantly changed the abundance of 13.79% of phyla and 10.32% of genera. In total, 38 ARG-like open reading frames (ORFs) and 327 ARG-like transcripts were identified in the DNA and RNA samples, respectively. The relative abundances of the total ARGs, each ARG type, and each ARG subtype also varied after UV disinfection. Additionally, UV disinfection significantly reduced the expression of total ARGs from 49.40 transcripts per kilobase of exon model per million mapped reads (TPM) to 47.62 TPM, and significantly changed the expression of 10.75% of ARG subtypes in wastewater (p < 0.05). Notably, the significant increase in the expression and obvious increase in the relative abundance of macrolide-lincosamide-streptogramin B (MLSB) resistance genes revealed that UV disinfection increases the potential health risk of MLSB resistance genes in wastewater. Moreover, potential host analyses of ARGs revealed the different preferences of antibiotic resistant bacteria (ARB) to ARGs. This study may shed new light on the underlying mechanism of the UV disinfection effect on antibiotic resistance.},
}
@article {pmid33277629,
year = {2020},
author = {Maghini, DG and Moss, EL and Vance, SE and Bhatt, AS},
title = {Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41596-020-00424-x},
pmid = {33277629},
issn = {1750-2799},
support = {R01AI148623//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AI143757//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P30 AG047366//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1S10OD02014101//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P30 CA124435/CA/NCI NIH HHS/United States ; DGE-114747//National Science Foundation (NSF)/ ; },
abstract = {Short-read metagenomic sequencing and de novo genome assembly of the human gut microbiome can yield draft bacterial genomes without isolation and culture. However, bacterial genomes assembled from short-read sequencing are often fragmented. Furthermore, these metagenome-assembled genomes often exclude repeated genomic elements, such as mobile genetic elements, compromising our understanding of the contribution of these elements to important bacterial phenotypes. Although long-read sequencing has been applied successfully to the assembly of contiguous bacterial isolate genomes, extraction of DNA of sufficient molecular weight, purity and quantity for metagenomic sequencing from stool samples can be challenging. Here, we present a protocol for the extraction of microgram quantities of high-molecular-weight DNA from human stool samples that are suitable for downstream long-read sequencing applications. We also present Lathe (www.github.com/bhattlab/lathe), a computational workflow for long-read basecalling, assembly, consensus refinement with long reads or Illumina short reads and genome circularization. Altogether, this protocol can yield high-quality contiguous or circular bacterial genomes from a complex human gut sample in approximately 10 d, with 2 d of hands-on bench and computational effort.},
}
@article {pmid33277434,
year = {2020},
author = {Reysenbach, AL and St John, E and Meneghin, J and Flores, GE and Podar, M and Dombrowski, N and Spang, A and L'Haridon, S and Humphris, SE and de Ronde, CEJ and Caratori Tontini, F and Tivey, M and Stucker, VK and Stewart, LC and Diehl, A and Bach, W},
title = {Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.2019021117},
pmid = {33277434},
issn = {1091-6490},
abstract = {Hydrothermally active submarine volcanoes are mineral-rich biological oases contributing significantly to chemical fluxes in the deep sea, yet little is known about the microbial communities inhabiting these systems. Here we investigate the diversity of microbial life in hydrothermal deposits and their metagenomics-inferred physiology in light of the geological history and resulting hydrothermal fluid paths in the subsurface of Brothers submarine volcano north of New Zealand on the southern Kermadec arc. From metagenome-assembled genomes we identified over 90 putative bacterial and archaeal genomic families and nearly 300 previously unknown genera, many potentially endemic to this submarine volcanic environment. While magmatically influenced hydrothermal systems on the volcanic resurgent cones of Brothers volcano harbor communities of thermoacidophiles and diverse members of the superphylum &quot;DPANN,&quot; two distinct communities are associated with the caldera wall, likely shaped by two different types of hydrothermal circulation. The communities whose phylogenetic diversity primarily aligns with that of the cone sites and magmatically influenced hydrothermal systems elsewhere are characterized predominately by anaerobic metabolisms. These populations are probably maintained by fluids with greater magmatic inputs that have interacted with different (deeper) previously altered mineral assemblages. However, proximal (a few meters distant) communities with gene-inferred aerobic, microaerophilic, and anaerobic metabolisms are likely supported by shallower seawater-dominated circulation. Furthermore, mixing of fluids from these two distinct hydrothermal circulation systems may have an underlying imprint on the high microbial phylogenomic diversity. Collectively our results highlight the importance of considering geologic evolution and history of subsurface processes in studying microbial colonization and community dynamics in volcanic environments.},
}
@article {pmid33277010,
year = {2020},
author = {Zhang, RM and Liu, X and Wang, SL and Fang, LX and Sun, J and Liu, YH and Liao, XP},
title = {Distribution patterns of antibiotic resistance genes and their bacterial hosts in pig farm wastewater treatment systems and soil fertilized with pig manure.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {143654},
doi = {10.1016/j.scitotenv.2020.143654},
pmid = {33277010},
issn = {1879-1026},
abstract = {Vast reservoirs of antibiotic resistance genes (ARG) are discharged into the environment via pig manure. We used metagenomic analysis to follow the distribution and shifts of ARGs and their bacterial hosts along wastewater treatment in three large pig farms. The predominating ARGs potentially encoded resistance to tetracycline (28.13%), aminoglycosides (23.64%), macrolide-lincosamide-streptogramin (MLS) (12.17%), sulfonamides (11.53%), multidrug (8.74%) and chloramphenicol (6.18%). The total relative ARG abundance increased along the treatment pathway prior to anaerobic digestion that had a similar degradative capacity for different ARGs and these ARGs were reduced by about 25% after digestion, but ARGs enriched erratically in manured soils. Distinctive ARG distribution patterns were found according to the three sample locations; feces, soil and wastewater and the differences were primarily due to the tetracycline ARGs (feces > wastewater > soil), sulfonamide ARGs (soil > wastewater > feces) and MLS ARGs (feces > wastewater > soil). Metagenomic assembly-based host analyses indicated the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were primary ARG carriers. The Streptococcaceae increased the abundance of multidrug, MLS and aminoglycoside ARGs in feces; Moraxellaceae were the primary contributors to the high abundance of multidrug ARGs in wastewater; the Comamonadaceae led to the higher abundance of bacA in wastewater and soil than feces. We found a high level of heterogeneity for both ARGs and ARG-hosts in the wastewater treatment system and in the agricultural soils for these pig farms.},
}
@article {pmid33276718,
year = {2020},
author = {Fan, Q and Wanapat, M and Yan, T and Hou, F},
title = {Altitude influences microbial diversity and herbage fermentation in the rumen of yaks.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {370},
pmid = {33276718},
issn = {1471-2180},
support = {2019QZKK0302//the Program for the Second Tibetan Plateau Scientific Expedition and Research: Grassland Ecosystem and Ecological Animal Husbandry/ ; 20200079//Research and Demonstration of Grassland Ecological Monitoring System in Gannan Plateau Pastoral Area/ ; IRT_17R50//Changjiang Scholars and Innovative Research Team in University/ ; },
abstract = {BACKGROUND: Rumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks (Bos grunniens) to fluctuating environments, especially the rumen microbiome. To address this, we investigated the diet, rumen bacterial community, and volatile fatty acids (VFA) of rumen fluid of yaks raised in the great Qinghai-Tibet plateau (QTP) at 2800 (low altitude, L), 3700 (middle altitude, M), and 4700 m (high altitude, H) above sea level.<br><br>RESULTS: The results showed that despite a partial diet overlap, H yaks harbored higher fibrous fractious contents than the M and L grazing yaks. Bacteria including Christensenellaceae_R-7_group, Ruminococcus_1, Romboutsia, Alloprevotella, Eubacterium coprostanoligenes, Clostridium, Streptococcus, and Treponema were found to be enriched in the rumen of yaks grazing at H. They also showed higher rumen microbial diversity and total VFA concentrations than those shown by yaks at M and L. Principal coordinates analysis (PCoA) on weighted UniFrac distances revealed that the bacterial community structure of rumen differed between the three altitudes. Moreover, Tax4fun metagenome estimation revealed that microbial genes associated with energy requirement and carbohydrate metabolic fate were overexpressed in the rumen microbiota of H yaks.<br><br>CONCLUSIONS: Collectively, our results revealed that H yaks had a stronger herbage fermenting ability via rumen microbial fermentation. Their enhanced ability of utilizing herbage may be partly owing to a microbiota adaptation for more energy requirements in the harsh H environment, such as lower temperature and the risk of hypoxia.},
}
@article {pmid33276717,
year = {2020},
author = {Gohl, DM and Garbe, J and Grady, P and Daniel, J and Watson, RHB and Auch, B and Nelson, A and Yohe, S and Beckman, KB},
title = {A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {863},
pmid = {33276717},
issn = {1471-2164},
mesh = {Benchmarking ; COVID-19/diagnosis/epidemiology/*virology ; COVID-19 Nucleic Acid Testing/*methods/standards ; Genome, Viral/*genetics ; Humans ; Molecular Epidemiology ; Mutation ; RNA, Viral/genetics ; SARS-CoV-2/*genetics/isolation &amp; purification ; Sequence Analysis/methods/standards ; },
abstract = {BACKGROUND: The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands of isolates are being sequenced around the world and deposited in public data repositories. A number of methods using both short- and long-read technologies are currently being applied for SARS-CoV-2 sequencing, including amplicon approaches, metagenomic methods, and sequence capture or enrichment methods. Given the small genome size, the ability to sequence SARS-CoV-2 at scale is limited by the cost and labor associated with making sequencing libraries.<br><br>RESULTS: Here we describe a low-cost, streamlined, all amplicon-based method for sequencing SARS-CoV-2, which bypasses costly and time-consuming library preparation steps. We benchmark this tailed amplicon method against both the ARTIC amplicon protocol and sequence capture approaches and show that an optimized tailed amplicon approach achieves comparable amplicon balance, coverage metrics, and variant calls to the ARTIC v3 approach.<br><br>CONCLUSIONS: The tailed amplicon method we describe represents a cost-effective and highly scalable method for SARS-CoV-2 sequencing.},
}
@article {pmid33273721,
year = {2020},
author = {Seyler, LM and Trembath-Reichert, E and Tully, BJ and Huber, JA},
title = {Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-020-00843-4},
pmid = {33273721},
issn = {1751-7370},
support = {OCE-1745589//National Science Foundation (NSF)/ ; OCE-1635208//National Science Foundation (NSF)/ ; C-DEBI OCE-0939564//Center for Dark Energy Biosphere Investigations (C-DEBI)/ ; GBMF1609//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
abstract = {The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.},
}
@article {pmid33273008,
year = {2020},
author = {Butina, TV and Petrushin, IS and Khanaev, IV and Bukin, YS},
title = {Virome Analysis of Near-Bottom Coastal Water of Lake Baikal.},
journal = {Microbiology resource announcements},
volume = {9},
number = {49},
pages = {},
pmid = {33273008},
issn = {2576-098X},
abstract = {In recent years, Lake Baikal has undergone significant changes in the composition of coastal communities associated with the increasing anthropogenic influence and global climate changes. In this context, we carried out metagenomic sequencing of the DNA viral community of an integral near-bottom water sample from the littoral zone of the lake.},
}
@article {pmid33272999,
year = {2020},
author = {Yemenian, T and Florea, KM and Thrash, JC and Webb, EA},
title = {Metagenome-Assembled Genome Sequence of Aphanizomenon flos-aquae Strain Clear-A1, Assembled from an Enrichment Culture.},
journal = {Microbiology resource announcements},
volume = {9},
number = {49},
pages = {},
pmid = {33272999},
issn = {2576-098X},
abstract = {Aphanizomenon flos-aquae is a significant harmful algal bloom-forming cyanobacterial species. Here, we report the draft genome for a strain of A. flos-aquae (Clear-A1) from a harmful algal bloom enrichment culture. This metagenome-assembled genome (MAG) sequence comprises 4,452,466 bp in 60 contigs with a GC content of 37.1%.},
}
@article {pmid33272998,
year = {2020},
author = {Florea, KM and Thrash, JC and Webb, EA},
title = {Metagenome-Assembled Genome Sequence of Dolichospermum circinale Strain Clear-D4, Assembled from a Harmful Cyanobacterial Bloom Enrichment Culture.},
journal = {Microbiology resource announcements},
volume = {9},
number = {49},
pages = {},
pmid = {33272998},
issn = {2576-098X},
abstract = {Dolichospermum circinale (formerly Anabaena circinale) is a significant harmful algal bloom species. We report the draft metagenome-assembled genome (MAG) for a strain of D. circinale (Clear-D4) obtained from an enrichment culture. The genome sequence comprises 5,029,933 bp in 560 contigs with a GC content of 37%.},
}
@article {pmid33272997,
year = {2020},
author = {Floback, AE and Florea, KM and Thrash, JC and Webb, EA},
title = {Metagenome-Assembled Genome Sequence of Vulcanococcus sp. Strain Clear-D1, Assembled from a Cyanobacterial Enrichment Culture.},
journal = {Microbiology resource announcements},
volume = {9},
number = {49},
pages = {},
pmid = {33272997},
issn = {2576-098X},
abstract = {We report the metagenome-assembled genome sequence of a Vulcanococcus sp. binned from a cyanobacterial enrichment culture. The genome contains 39 contigs comprising 2.96 Mbp and is estimated as 100% complete, with a GC content of 63.9% and 3,261 predicted coding genes.},
}
@article {pmid33272996,
year = {2020},
author = {Cheng, C and Florea, KM and Webb, EA and Thrash, JC},
title = {Metagenome-Assembled Genome Sequence of Rhodobacteraceae Bacterium Strain Clear-D3, Assembled from a Dolichospermum Consortium from Clear Lake, California.},
journal = {Microbiology resource announcements},
volume = {9},
number = {49},
pages = {},
pmid = {33272996},
issn = {2576-098X},
abstract = {Here, we report the metagenome-assembled genome sequence of a Rhodobacteraceae bacterium strain, Clear-D3, that was reconstructed from a cyanobacterial enrichment from a eutrophic lake. The draft genome sequence shows evidence of an anoxygenic photoautotrophic lifestyle. Other potential capabilities include aerobic heterotrophy, flagellar motility, chemotaxis, and utilization of complex C-P compounds.},
}
@article {pmid33272995,
year = {2020},
author = {Al-Saud, S and Florea, KM and Webb, EA and Thrash, JC},
title = {Metagenome-Assembled Genome Sequence of Kapabacteriales Bacterium Strain Clear-D13, Assembled from a Harmful Algal Bloom Enrichment Culture.},
journal = {Microbiology resource announcements},
volume = {9},
number = {49},
pages = {},
pmid = {33272995},
issn = {2576-098X},
abstract = {Metagenomic sequencing of a Dolichospermum circinale enrichment culture resulted in the assembly of several cocultured metagenome-assembled genomes (MAGs). One MAG was affiliated with the class Kapabacteriales and included 5,724,991 bp in 127 contigs with a GC content of 48.4%.},
}
@article {pmid33272993,
year = {2020},
author = {Babalola, OO and Chukwuneme, CF and Ayangbenro, AS},
title = {Shotgun Sequencing Revealed the Microbiota of Zea mays Rhizosphere of a Former Grassland and an Intensively Cultivated Agricultural Land.},
journal = {Microbiology resource announcements},
volume = {9},
number = {49},
pages = {},
pmid = {33272993},
issn = {2576-098X},
abstract = {Land use is a major factor contributing to the differences in soil microbial assemblages. Despite the importance of microbial communities on crop health and productivity, a knowledge gap exists on the effects of land use change on microbial functions in the rhizosphere. This data set presents the metagenomic data from two maize fields in South Africa with different agricultural histories. It provides an opportunity for modeling microbes with beneficial functions that could enhance crop productivity.},
}
@article {pmid33272988,
year = {2020},
author = {Singh, RP and Johri, AK and Dua, M},
title = {Metagenomic Analysis of Microbial Diversity in Cotton Rhizosphere Soil in Alwar, India.},
journal = {Microbiology resource announcements},
volume = {9},
number = {49},
pages = {},
pmid = {33272988},
issn = {2576-098X},
abstract = {Cotton is an important cash crop for both the Indian economy and rural livelihoods. In the present study, metagenomic analysis is used to characterize microbial diversity in cotton rhizosphere soil from the Alwar district, located in the semiarid northeast region of the state of Rajasthan in India.},
}
@article {pmid33272789,
year = {2020},
author = {Muñoz-Benavent, M and Pérez-Cobas, AE and García-Ferris, C and Moya, A and Latorre, A},
title = {Insects' potential: Understanding the functional role of their gut microbiome.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {},
number = {},
pages = {113787},
doi = {10.1016/j.jpba.2020.113787},
pmid = {33272789},
issn = {1873-264X},
abstract = {The study of insect-associated microbial communities is a field of great importance in agriculture, principally because of the role insects play as pests. In addition, there is a recent focus on the potential of the insect gut microbiome in areas such as biotechnology, given some microorganisms produce molecules with biotechnological and industrial applications, and also in biomedicine, since some bacteria and fungi are a reservoir of antibiotic resistance genes (ARGs). To date, most studies aiming to characterize the role of the gut microbiome of insects have been based on high-throughput sequencing of the 16S rRNA gene and/or metagenomics. However, recently functional approaches such as metatranscriptomics, metaproteomics and metabolomics have also been employed. Besides providing knowledge about the taxonomic distribution of microbial populations, these techniques also reveal their functional and metabolic capabilities. This information is essential to gain a better understanding of the role played by microbes comprising the microbial communities in their hosts, as well as to indicate their possible exploitation. This review provides an overview of how far we have come in characterizing insect gut functionality through omics, as well as the challenges and future perspectives in this field.},
}
@article {pmid33272203,
year = {2020},
author = {Zhang, Q and Dao, T},
title = {A distance based multisample test for high-dimensional compositional data with applications to the human microbiome.},
journal = {BMC bioinformatics},
volume = {21},
number = {Suppl 9},
pages = {205},
pmid = {33272203},
issn = {1471-2105},
mesh = {Aged ; Bayes Theorem ; Computer Simulation ; Humans ; Metagenomics ; *Microbiota ; Middle Aged ; Numerical Analysis, Computer-Assisted ; },
abstract = {BACKGROUND: Compositional data refer to the data that lie on a simplex, which are common in many scientific domains such as genomics, geology and economics. As the components in a composition must sum to one, traditional tests based on unconstrained data become inappropriate, and new statistical methods are needed to analyze this special type of data.<br><br>RESULTS: In this paper, we consider a general problem of testing for the compositional difference between K populations. Motivated by microbiome and metagenomics studies, where the data are often over-dispersed and high-dimensional, we formulate a well-posed hypothesis from a Bayesian point of view and suggest a nonparametric test based on inter-point distance to evaluate statistical significance. Unlike most existing tests for compositional data, our method does not rely on any data transformation, sparsity assumption or regularity conditions on the covariance matrix, but directly analyzes the compositions. Simulated data and two real data sets on the human microbiome are used to illustrate the promise of our method.<br><br>CONCLUSIONS: Our simulation studies and real data applications demonstrate that the proposed test is more sensitive to the compositional difference than the mean-based method, especially when the data are over-dispersed or zero-inflated. The proposed test is easy to implement and computationally efficient, facilitating its application to large-scale datasets.},
}
@article {pmid33270717,
year = {2020},
author = {Skarżyńska, M and Leekitcharoenphon, P and Hendriksen, RS and Aarestrup, FM and Wasyl, D},
title = {A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0242987},
pmid = {33270717},
issn = {1932-6203},
abstract = {Antimicrobial resistance (AMR) in bacteria is a complex subject, why one need to look at this phenomenon from a wider and holistic perspective. The extensive use of the same antimicrobial classes in human and veterinary medicine as well as horticulture is one of the main drivers for the AMR selection. Here, we applied shotgun metagenomics to investigate the AMR epidemiology in several animal species including farm animals, which are often exposed to antimicrobial treatment opposed to an unique set of wild animals that seems not to be subjected to antimicrobial pressure. The comparison of the domestic and wild animals allowed to investigate the possible anthropogenic impact on AMR spread. Inclusion of animals with different feeding behaviors (carnivores, omnivores) enabled to further assess which AMR genes that thrives within the food chain. We tested fecal samples not only of intensively produced chickens, turkeys, and pigs, but also of wild animals such as wild boars, red foxes, and rodents. A multi-directional approach mapping obtained sequences to several databases provided insight into the occurrence of the different AMR genes. The method applied enabled also analysis of other factors that may influence AMR of intestinal microbiome such as diet. Our findings confirmed higher levels of AMR in farm animals than in wildlife. The results also revealed the potential of wildlife in the AMR dissemination. Particularly in red foxes, we found evidence of several AMR genes conferring resistance to critically important antimicrobials like quinolones and cephalosporins. In contrast, the lowest abundance of AMR was observed in rodents originating from natural environment with presumed limited exposure to antimicrobials. Shotgun metagenomics enabled us to demonstrate that discrepancies between AMR profiles found in the intestinal microbiome of various animals probably resulted from the different antimicrobial exposure, habitats, and behavior of the tested animal species.},
}
@article {pmid33270378,
year = {2020},
author = {Gatcliffe, C and Rao, A and Brigger, M and Dimmock, D and Hansen, C and Montgomery, J and Schlaberg, R and Coufal, NG and Farnaes, L},
title = {Metagenomic sequencing and evaluation of the host response in the pediatric aerodigestive population.},
journal = {Pediatric pulmonology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ppul.25198},
pmid = {33270378},
issn = {1099-0496},
abstract = {OBJECTIVES: To assess the diagnostic utility of metagenomic sequencing in pediatric aerodigestive clinic patients being evaluated for chronic aspiration. We hypothesize that using a metagenomics platform will aid in the identification of microbes not found on standard culture.<br><br>STUDY DESIGN AND METHODS: Twenty-four children referred to an aerodigestive clinic were enrolled in a prospective, single-site, cross-sectional cohort study. At the time of clinical evaluation under anesthesia, two samples were obtained: an upper airway sample and a sample from bronchoalveolar lavage (BAL). Samples were sent for routine culture and analyzed using Explify® Respiratory, a CLIA Laboratory Developed Test which identifies respiratory commensals and pathogens through RNA and DNA sequencing. Since RNA was sequenced in the course of the metagenomic analysis to identify organisms (RNA viruses and bacteria), the sequencing approach also captured host derived messenger RNA during sample analysis. This incidentally obtained host transcriptomic data were analyzed to evaluate the host immune response. The results of these studies were correlated with the clinical presentation of the research subjects.<br><br>RESULTS: In 10 patients, organisms primarily associated with oral flora were identified in the BAL. Standard culture was negative in three patients where clinical metagenomics led to a result with potential clinical significance. Transcriptomic data correlated with the presence or absence of dysphagia as identified on prior videofluoroscopic evaluation of swallowing.<br><br>CONCLUSIONS: Clinical metagenomics allows for simultaneous analysis of the microbiota and the host immune response from BAL samples. As the technologies in this field continue to advance, such testing may improve the diagnostic evaluation of patients with suspected chronic aspiration.},
}
@article {pmid33268597,
year = {2020},
author = {Limeta, A and Ji, B and Levin, M and Gatto, F and Nielsen, J},
title = {Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma.},
journal = {JCI insight},
volume = {5},
number = {23},
pages = {},
pmid = {33268597},
issn = {2379-3708},
abstract = {BACKGROUNDIdentifying factors conferring responses to therapy in cancer is critical to select the best treatment for patients. For immune checkpoint inhibition (ICI) therapy, mounting evidence suggests that the gut microbiome can determine patient treatment outcomes. However, the extent to which gut microbial features are applicable across different patient cohorts has not been extensively explored.METHODSWe performed a meta-analysis of 4 published shotgun metagenomic studies (Ntot = 130 patients) investigating differential microbiome composition and imputed metabolic function between responders and nonresponders to ICI.RESULTSOur analysis identified both known microbial features enriched in responders, such as Faecalibacterium as the prevailing taxa, as well as additional features, including overrepresentation of Barnesiella intestinihominis and the components of vitamin B metabolism. A classifier designed to predict responders based on these features identified responders in an independent cohort of 27 patients with the area under the receiver operating characteristic curve of 0.625 (95% CI: 0.348-0.899) and was predictive of prognosis (HR = 0.35, P = 0.081).CONCLUSIONThese results suggest the existence of a fecal microbiome signature inherent across responders that may be exploited for diagnostic or therapeutic purposes.FUNDINGThis work was funded by the Knut and Alice Wallenberg Foundation, BioGaia AB, and Cancerfonden.},
}
@article {pmid33268508,
year = {2020},
author = {Rom, O and Liu, Y and Liu, Z and Zhao, Y and Wu, J and Ghrayeb, A and Villacorta, L and Fan, Y and Chang, L and Wang, L and Liu, C and Yang, D and Song, J and Rech, JC and Guo, Y and Wang, H and Zhao, G and Liang, W and Koike, Y and Lu, H and Koike, T and Hayek, T and Pennathur, S and Xi, C and Wen, B and Sun, D and Garcia-Barrio, MT and Aviram, M and Gottlieb, E and Mor, I and Liu, W and Zhang, J and Chen, YE},
title = {Glycine-based treatment ameliorates NAFLD by modulating fatty acid oxidation, glutathione synthesis, and the gut microbiome.},
journal = {Science translational medicine},
volume = {12},
number = {572},
pages = {},
doi = {10.1126/scitranslmed.aaz2841},
pmid = {33268508},
issn = {1946-6242},
support = {R01 HL123333/HL/NHLBI NIH HHS/United States ; },
abstract = {Nonalcoholic fatty liver disease (NAFLD) including nonalcoholic steatohepatitis (NASH) has reached epidemic proportions with no pharmacological therapy approved. Lower circulating glycine is consistently reported in patients with NAFLD, but the causes for reduced glycine, its role as a causative factor, and its therapeutic potential remain unclear. We performed transcriptomics in livers from humans and mice with NAFLD and found suppression of glycine biosynthetic genes, primarily alanine-glyoxylate aminotransferase 1 (AGXT1). Genetic (Agxt1-/- mice) and dietary approaches to limit glycine availability resulted in exacerbated diet-induced hyperlipidemia and steatohepatitis, with suppressed mitochondrial/peroxisomal fatty acid β-oxidation (FAO) and enhanced inflammation as the underlying pathways. We explored glycine-based compounds with dual lipid/glucose-lowering properties as potential therapies for NAFLD and identified a tripeptide (Gly-Gly-L-Leu, DT-109) that improved body composition and lowered circulating glucose, lipids, transaminases, proinflammatory cytokines, and steatohepatitis in mice with established NASH induced by a high-fat, cholesterol, and fructose diet. We applied metagenomics, transcriptomics, and metabolomics to explore the underlying mechanisms. The bacterial genus Clostridium sensu stricto was markedly increased in mice with NASH and decreased after DT-109 treatment. DT-109 induced hepatic FAO pathways, lowered lipotoxicity, and stimulated de novo glutathione synthesis. In turn, inflammatory infiltration and hepatic fibrosis were attenuated via suppression of NF-κB target genes and TGFβ/SMAD signaling. Unlike its effects on the gut microbiome, DT-109 stimulated FAO and glutathione synthesis independent of NASH. In conclusion, impaired glycine metabolism may play a causative role in NAFLD. Glycine-based treatment attenuates experimental NAFLD by stimulating hepatic FAO and glutathione synthesis, thus warranting clinical evaluation.},
}
@article {pmid33268363,
year = {2020},
author = {Yang, J and Zheng, P and Li, Y and Wu, J and Tan, X and Zhou, J and Sun, Z and Chen, X and Zhang, G and Zhang, H and Huang, Y and Chai, T and Duan, J and Liang, W and Yin, B and Lai, J and Huang, T and Du, Y and Zhang, P and Jiang, J and Xi, C and Wu, L and Lu, J and Mou, T and Xu, Y and Perry, SW and Wong, ML and Licinio, J and Hu, S and Wang, G and Xie, P},
title = {Landscapes of bacterial and metabolic signatures and their interaction in major depressive disorders.},
journal = {Science advances},
volume = {6},
number = {49},
pages = {},
pmid = {33268363},
issn = {2375-2548},
abstract = {Gut microbiome disturbances have been implicated in major depressive disorder (MDD). However, little is known about how the gut virome, microbiome, and fecal metabolome change, and how they interact in MDD. Here, using whole-genome shotgun metagenomic and untargeted metabolomic methods, we identified 3 bacteriophages, 47 bacterial species, and 50 fecal metabolites showing notable differences in abundance between MDD patients and healthy controls (HCs). Patients with MDD were mainly characterized by increased abundance of the genus Bacteroides and decreased abundance of the genera Blautia and Eubacterium These multilevel omics alterations generated a characteristic MDD coexpression network. Disturbed microbial genes and fecal metabolites were consistently mapped to amino acid (γ-aminobutyrate, phenylalanine, and tryptophan) metabolism. Furthermore, we identified a combinatorial marker panel that robustly discriminated MDD from HC individuals in both the discovery and validation sets. Our findings provide a deep insight into understanding of the roles of disturbed gut ecosystem in MDD.},
}
@article {pmid33264956,
year = {2021},
author = {Guo, H and Gu, J and Wang, X and Song, Z and Qian, X and Sun, W and Nasir, M and Yu, J},
title = {Negative effects of oxytetracycline and copper on nitrogen metabolism in an aerobic fermentation system: Characteristics and mechanisms.},
journal = {Journal of hazardous materials},
volume = {403},
number = {},
pages = {123890},
doi = {10.1016/j.jhazmat.2020.123890},
pmid = {33264956},
issn = {1873-3336},
abstract = {Aerobic fermentation is a sustainable option for livestock waste treatment, but little is known about the microbial mechanism that allows oxytetracycline (OTC) and copper (Cu) to affect nitrogen metabolism during aerobic fermentation. In this study, contamination with OTC and Cu alone or in combination reduced the total nitrogen (TN) content of the fermentation products. Metagenomic analysis demonstrated that the contribution of microorganisms to nitrogen metabolism changed significantly in different stages of fermentation. OTC and Cu affected the formation and utilization pattern of NO2--N by microorganisms, which were mainly responsible for the reduced N2O emissions. In the presence of OTC and/or Cu, Myxococcus_stipitatus, Myxococcus_xanthus, and Gimesia_maris were evidently enriched at the end of fermentation, and their increased roles in the dissimilatory reduction of nitrite to ammonium were confirmed by network analysis. Ardenticatena_maritima was the main contributor to denitrification (NO3--N to NO). Furthermore, organic matter (OM) was the most important factor responsible for driving the variation in nitrogen-transforming microorganisms and controlling denitrification. OTC affected the formation of OM, which can directly affect TN (λ = -0.37, p < 0.001), and the adverse impact of Cu on nirK- and nifH-dominant microorganisms was validated (p < 0.05).},
}
@article {pmid33264437,
year = {2020},
author = {Kim, SS and Eun, JW and Cho, HJ and Song, DS and Kim, CW and Kim, YS and Lee, SW and Kim, YK and Yang, J and Choi, J and Yim, HJ and Cheong, JY},
title = {Microbiome as a potential diagnostic and predictive biomarker in severe alcoholic hepatitis.},
journal = {Alimentary pharmacology &amp; therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.16200},
pmid = {33264437},
issn = {1365-2036},
support = {//The Research Supporting Program of The Korean Association for the Study of the Liver and The Korean Liver Foundation/ ; NRF-2018M3A9E8023861//National Research Foundation of Korea/ ; NRF-2019R1C1C1004580//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Severe alcoholic hepatitis (AH) is the most aggressive form of alcohol-related liver disease with high mortality. The microbiome is an emerging therapeutic target in alcohol-related liver disease.<br><br>AIMS: To investigate the microbiome composition in patients with severe AH, and to determine microbiome recovery after rifaximin treatment in gut bacteria and bacteria derived-extracellular vesicles.<br><br>METHODS: We enrolled 24 patients with severe AH and 24 healthy controls. Additional faecal samples were collected after 4 weeks in 8 patients with severe AH who completed rifaximin treatment. Treatment response was defined based on Lille score model after 7 days of treatment. Metagenomic profiling was performed using 16S ribosomal RNA amplicon sequencing.<br><br>RESULTS: Faecal microbiomes of patients with severe AH had lower alpha diversity and higher beta diversity than those of healthy controls in both gut bacteria and extracellular vesicles. Bacilli, Lactobacillales and Veillonella were significantly increased in the gut bacteria of patients with severe AH, and Veillonella, Veillonella parvula group and Lactobacillales were significantly increased in the extracellular vesicles of patients with severe AH. Eubacterium_g23, Oscillibacter and Clostridiales decreased in the gut bacteria of patients with severe AH, and Eubacterium_g23, Oscillibacter and Christensenellaceae decreased in the extracellular vesicles of patients with severe AH. After rifaximin treatment, 17 taxa in the gut bacteria and 23 taxa in extracellular vesicles were significantly restored in patients with severe AH. In common, Veillonella and Veillonella parvula group increased in patients with severe AH and decreased after rifaximin treatment, and Prevotella and Prevotellaceae decreased in patients with severe AH and increased after rifaximin treatment. Treatment non-responders showed a significantly lower abundance of Prevotella at baseline than did treatment responders.<br><br>CONCLUSION: Dysbiosis was confirmed in severe AH but was alleviated by rifaximin treatment. Taxa associated with severe AH can be candidate biomarkers or therapeutic targets.},
}
@article {pmid33264351,
year = {2020},
author = {Ekman, L and Bagge, E and Nyman, A and Persson Waller, K and Pringle, M and Segerman, B},
title = {A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0242880},
pmid = {33264351},
issn = {1932-6203},
abstract = {Udder cleft dermatitis (UCD) is a skin condition affecting the fore udder attachment of dairy cows. UCD may be defined as mild (eczematous skin changes) or severe (open wounds, large skin changes). Our aims were to compare the microbiota of mild and severe UCD lesions with the microbiota of healthy skin from the fore udder attachment of control cows, and to investigate whether mastitis-causing pathogens are present in UCD lesions. Samples were obtained from cows in six dairy herds. In total, 36 UCD samples categorized as mild (n = 17) or severe (n = 19) and 13 control samples were sequenced using a shotgun metagenomic approach and the reads were taxonomically classified based on their k-mer content. The Wilcoxon rank sum test was used to compare the abundance of different taxa between different sample types, as well as to compare the bacterial diversity between samples. A high proportion of bacteria was seen in all samples. Control samples had a higher proportion of archaeal reads, whereas most samples had low proportions of fungi, protozoa and viruses. The bacterial microbiota differed between controls and mild and severe UCD samples in both composition and diversity. Subgroups of UCD samples were visible, characterized by increased proportion of one or a few bacterial genera or species, e.g. Corynebacterium, Staphylococcus, Brevibacterium luteolum, Trueperella pyogenes and Fusobacterium necrophorum. Bifidobacterium spp. were more common in controls compared to UCD samples. The bacterial diversity was higher in controls compared to UCD samples. Bacteria commonly associated with mastitis were uncommon. In conclusion, a dysbiosis of the microbiota of mild and severe UCD samples was seen, characterized by decreased diversity and an increased proportion of certain bacteria. There was no evidence of a specific pathogen causing UCD or that UCD lesions are important reservoirs for mastitis-causing bacteria.},
}
@article {pmid33262957,
year = {2020},
author = {de Almeida, OGG and Capizzani, CPDC and Tonani, L and Grizante Barião, PH and da Cunha, AF and De Martinis, ECP and Torres, LAGMM and von Zeska Kress, MR},
title = {The Lung Microbiome of Three Young Brazilian Patients With Cystic Fibrosis Colonized by Fungi.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {598938},
pmid = {33262957},
issn = {2235-2988},
abstract = {Microbial communities infiltrate the respiratory tract of cystic fibrosis patients, where chronic colonization and infection lead to clinical decline. This report aims to provide an overview of the diversity of bacterial and fungal species from the airway secretion of three young CF patients with severe pulmonary disease. The bacterial and fungal microbiomes were investigated by culture isolation, metataxonomics, and metagenomics shotgun. Virulence factors and antibiotic resistance genes were also explored. A. fumigatus was isolated from cultures and identified in high incidence from patient sputum samples. Candida albicans, Penicillium sp., Hanseniaspora sp., Torulaspora delbrueckii, and Talaromyces amestolkiae were isolated sporadically. Metataxonomics and metagenomics detected fungal reads (Saccharomyces cerevisiae, A. fumigatus, and Schizophyllum sp.) in one sputum sample. The main pathogenic bacteria identified were Staphylococcus aureus, Pseudomonas aeruginosa, Burkholderia cepacia complex, and Achromobacter xylosoxidans. The canonical core CF microbiome is composed of species from the genera Streptococcus, Neisseria, Rothia, Prevotella, and Haemophilus. Thus, the airways of the three young CF patients presented dominant bacterial genera and interindividual variability in microbial community composition and diversity. Additionally, a wide diversity of virulence factors and antibiotic resistance genes were identified in the CF lung microbiomes, which may be linked to the clinical condition of the CF patients. Understanding the microbial community is crucial to improve therapy because it may have the opposite effect, restructuring the pathogenic microbiota. Future studies focusing on the influence of fungi on bacterial diversity and microbial interactions in CF microbiomes will be welcome to fulfill this huge gap of fungal influence on CF physiopathology.},
}
@article {pmid33262743,
year = {2020},
author = {Gwak, HJ and Rho, M},
title = {Data-Driven Modeling for Species-Level Taxonomic Assignment From 16S rRNA: Application to Human Microbiomes.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {570825},
pmid = {33262743},
issn = {1664-302X},
abstract = {With the emergence of next-generation sequencing (NGS) technology, there have been a large number of metagenomic studies that estimated the bacterial composition via 16S ribosomal RNA (16S rRNA) amplicon sequencing. In particular, subsets of the hypervariable regions in 16S rRNA, such as V1-V2 and V3-V4, are targeted using high-throughput sequencing. The sequences from different taxa are assigned to a specific taxon based on the sequence homology. Since such sequences are highly homologous or identical between species in the same genus, it is challenging to determine the exact species using 16S rRNA sequences only. Therefore, in this study, homologous species groups were defined to obtain maximum resolution related with species using 16S rRNA. For the taxonomic assignment using 16S rRNA, three major 16S rRNA databases are independently used since the lineage of certain bacteria is not consistent among these databases. On the basis of the NCBI taxonomy classification, we re-annotated inconsistent lineage information in three major 16S rRNA databases. For each species, we constructed a consensus sequence model for each hypervariable region and determined homologous species groups that consist of indistinguishable species in terms of sequence homology. Using a k-nearest neighbor method and the species consensus sequence models, the species-level taxonomy was determined. If the species determined is a member of homologous species groups, the species group is assigned instead of a specific species. Notably, the results of the evaluation on our method using simulated and mock datasets showed a high correlation with the real bacterial composition. Furthermore, in the analysis of real microbiome samples, such as salivary and gut microbiome samples, our method successfully performed species-level profiling and identified differences in the bacterial composition between different phenotypic groups.},
}
@article {pmid33262428,
year = {2020},
author = {Gharechahi, J and Vahidi, MF and Bahram, M and Han, JL and Ding, XZ and Salekdeh, GH},
title = {Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-020-00837-2},
pmid = {33262428},
issn = {1751-7370},
abstract = {Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated cattle. Our metagenome sequencing provided novel genomic insights into functional potential of 523 uncultured bacteria and 15 mostly uncultured archaea in the rumen. The assembled genomes belonged mainly to Bacteroidota, Firmicutes, Verrucomicrobiota, and Fibrobacterota and were enriched for genes related to the degradation of lignocellulosic polymers and the fermentation of degraded products into short chain volatile fatty acids. We also found a shift from copiotrophic to oligotrophic taxa during the course of rumen fermentation, potentially important for the digestion of recalcitrant lignocellulosic substrates in the physiochemically complex and varying environment of the rumen. Differential colonization of forages (the incubated lignocellulosic materials) by rumen microbiota suggests that taxonomic and metabolic diversification is an evolutionary adaptation to diverse lignocellulosic substrates constituting a major component of the cattle's diet. Our data also provide novel insights into the key role of unique microbial diversity and associated gene functions in the degradation of recalcitrant lignocellulosic materials in the rumen.},
}
@article {pmid33261862,
year = {2020},
author = {Liu, D and Legras, JL and Zhang, P and Chen, D and Howell, K},
title = {Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine.},
journal = {International journal of food microbiology},
volume = {},
number = {},
pages = {108983},
doi = {10.1016/j.ijfoodmicro.2020.108983},
pmid = {33261862},
issn = {1879-3460},
abstract = {Microbial ecology is an integral part of an agricultural ecosystem and influences the quality of agricultural commodities. Microbial activity influences grapevine health and crop production, conversion of sugar to ethanol during fermentation, thus forming wine aroma and flavour. There are regionally differentiated microbial patterns in grapevines and must but how microbial patterns contribute to wine regional distinctiveness (terroir) at small scale (<100 km) is not well defined. Here we characterise fungal communities, yeast populations, and Saccharomyces cerevisiae populations during spontaneous fermentation using metagenomics and population genetics to investigate microbial distribution and fungal contributions to the resultant wine. We found differentiation of fungi, yeasts, and S. cerevisiae between geographic origins (estate/vineyard), with influences from the grape variety. Growth and dominance of S. cerevisiae during fermentation reshaped the fungal community and showed geographic structure at the strain level. Associations between fungal microbiota diversity and wine chemicals suggest that S. cerevisiae plays a primary role in determining wine aroma profiles at a sub-regional scale. The geographic distribution at scales of less than 12 km supports that differential microbial communities, including the dominant fermentative yeast S. cerevisiae can be distinct in a local setting. These findings provide further evidence for microbial contributions to wine terroir, and perspectives for sustainable agricultural practices to maintain microbial diversity and optimise fermentation function to craft beverage quality.},
}
@article {pmid33261720,
year = {2021},
author = {Solomon, IH and Ganesh, VS and Yu, G and Deng, XD and Wilson, MR and Miller, S and Milligan, TA and Mukerji, SS and Mathewson, A and Linxweiler, J and Morse, D and Ritter, JM and Staples, JE and Hughes, H and Gould, CV and Sabeti, PC and Chiu, CY and Piantadosi, A},
title = {Fatal Case of Chronic Jamestown Canyon Virus Encephalitis Diagnosed by Metagenomic Sequencing in Patient Receiving Rituximab.},
journal = {Emerging infectious diseases},
volume = {27},
number = {1},
pages = {},
pmid = {33261720},
issn = {1080-6059},
abstract = {A 56-year-old man receiving rituximab who had months of neurologic symptoms was found to have Jamestown Canyon virus in cerebrospinal fluid by clinical metagenomic sequencing. The patient died, and postmortem examination revealed extensive neuropathologic abnormalities. Deep sequencing enabled detailed characterization of viral genomes from the cerebrospinal fluid, cerebellum, and cerebral cortex.},
}
@article {pmid33260993,
year = {2020},
author = {Hernández, M and Vera-Gargallo, B and Calabi-Floody, M and King, GM and Conrad, R and Tebbe, CC},
title = {Reconstructing Genomes of Carbon Monoxide Oxidisers in Volcanic Deposits Including Members of the Class Ktedonobacteria.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33260993},
issn = {2076-2607},
support = {Research Fellowship//Alexander von Humboldt-Stiftung/ ; },
abstract = {Microorganisms can potentially colonise volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H2) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of 380, 269 and 63 years, respectively. A total of 19 metagenome-assembled genomes (MAGs) were retrieved from all stages with a higher number observed in the youngest soil (1640: 2 MAGs, 1751: 1 MAG, 1957: 16 MAGs). Genomic similarity indices showed that several MAGs had amino-acid identity (AAI) values >50% to the phyla Actinobacteria, Acidobacteria, Gemmatimonadetes, Proteobacteria and Chloroflexi. Three MAGs from the youngest site (1957) belonged to the class Ktedonobacteria (Chloroflexi). Complete cellular functions of all the MAGs were characterised, including carbon fixation, terpenoid backbone biosynthesis, formate oxidation and CO oxidation. All 19 environmental genomes contained at least one gene encoding a putative carbon monoxide dehydrogenase (CODH). Three MAGs had form I coxL operon (encoding the large subunit CO-dehydrogenase). One of these MAGs (MAG-1957-2.1, Ktedonobacterales) was highly abundant in the youngest soil. MAG-1957-2.1 also contained genes encoding a [NiFe]-hydrogenase and hyp genes encoding accessory enzymes and proteins. Little is known about the Ktedonobacterales through cultivated isolates, but some species can utilise H2 and CO for growth. Our results strongly suggest that the remote volcanic sites in Chile represent a natural habitat for Ktedonobacteria and they may use reduced gases for growth.},
}
@article {pmid33260903,
year = {2020},
author = {Schuele, L and Cassidy, H and Lizarazo, E and Strutzberg-Minder, K and Schuetze, S and Loebert, S and Lambrecht, C and Harlizius, J and Friedrich, AW and Peter, S and Niesters, HGM and Rossen, JWA and Couto, N},
title = {Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples.},
journal = {Viruses},
volume = {12},
number = {12},
pages = {},
pmid = {33260903},
issn = {1999-4915},
abstract = {Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative.},
}
@article {pmid33260881,
year = {2020},
author = {Lancaster, SM and Sanghi, A and Wu, S and Snyder, MP},
title = {A Customizable Analysis Flow in Integrative Multi-Omics.},
journal = {Biomolecules},
volume = {10},
number = {12},
pages = {},
pmid = {33260881},
issn = {2218-273X},
abstract = {The number of researchers using multi-omics is growing. Though still expensive, every year it is cheaper to perform multi-omic studies, often exponentially so. In addition to its increasing accessibility, multi-omics reveals a view of systems biology to an unprecedented depth. Thus, multi-omics can be used to answer a broad range of biological questions in finer resolution than previous methods. We used six omic measurements-four nucleic acid (i.e., genomic, epigenomic, transcriptomics, and metagenomic) and two mass spectrometry (proteomics and metabolomics) based-to highlight an analysis workflow on this type of data, which is often vast. This workflow is not exhaustive of all the omic measurements or analysis methods, but it will provide an experienced or even a novice multi-omic researcher with the tools necessary to analyze their data. This review begins with analyzing a single ome and study design, and then synthesizes best practices in data integration techniques that include machine learning. Furthermore, we delineate methods to validate findings from multi-omic integration. Ultimately, multi-omic integration offers a window into the complexity of molecular interactions and a comprehensive view of systems biology.},
}
@article {pmid33260795,
year = {2020},
author = {Zhu, FC and Lian, CA and He, LS},
title = {Genomic Characterization of a Novel Tenericutes Bacterium from Deep-Sea Holothurian Intestine.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33260795},
issn = {2076-2607},
support = {2018YFC0309804//National Key Research and Development Program of China/ ; 2016YFC0302504//National Key Research and Development Program of China/ ; 2016YFC0304905//National Key Research and Development Program of China/ ; },
abstract = {Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and immunity of animals, but little is known about the composition and function of intestinal microbiota in deep-sea invertebrates. In this study, the intestinal microbiota of six holothurian Molpadia musculus were investigated, showing that their midguts were predominantly occupied by Izemoplasmatales bacteria. Using metagenomic sequencing, a draft genome of 1,822,181 bp was successfully recovered. After comparison with phylogenetically related bacteria, genes involved in saccharide usage and de novo nucleotide biosynthesis were reduced. However, a set of genes responsible for extracellular nucleoside utilization and 14 of 20 amino acid synthesis pathways were completely retained. Under oligotrophic condition, the gut-associated bacterium may make use of extracellular DNA for carbon and energy supplement, and may provide essential amino acids to the host. The clustered regularly interspaced short palindromic repeat (CRISPR) and restriction-modification (RM) systems presented in the genome may provide protection against invading viruses. A linear azol(in)e-containing peptide gene cluster for bacteriocin synthesize was also identified, which may inhibit the colonization and growth of harmful bacteria. Known virulence factors were not found by database searching. On the basis of its phylogenetic position and metabolic characteristics, we proposed that the bacterium represented a novel genus and a novel family within the Izemoplasmatales order and suggested it be named &quot;Candidatus Bathyoplasma sp. NZ&quot;. This was the first time describing host-associated Izemoplasmatales.},
}
@article {pmid33260452,
year = {2020},
author = {Lattos, A and Giantsis, IA and Karagiannis, D and Theodorou, JA and Michaelidis, B},
title = {Gut Symbiotic Microbial Communities in the IUCN Critically Endangered Pinna nobilis Suffering from Mass Mortalities, Revealed by 16S rRNA Amplicon NGS.},
journal = {Pathogens (Basel, Switzerland)},
volume = {9},
number = {12},
pages = {},
pmid = {33260452},
issn = {2076-0817},
abstract = {Mass mortality events due to disease outbreaks have recently affected almost every healthy population of fan mussel, Pinna nobilis in Mediterranean Sea. The devastating mortality of the species has turned the interest of the research towards the causes of these events. After the haplosporidan infestation and the infection by Mycobacterium sp., new emerging pathogens have arisen based on the latest research. In the present study, a metagenomic approach of 16S rRNA next generation sequencing (NGS) was applied in order to assess the bacterial diversity within the digestive gland of diseased individuals as well as to carry out geographical correlations among the biodiversity of microbiome in the endangered species Pinna nobilis. The specimens originated from the mortalities occurred in 2019 in the region of Greece. Together with other bacterial genera, the results confirmed the presence of Vibrio spp., assuming synergistic effects in the mortality events of the species. Alongside with the presence of Vibrio spp., numerous bacterial genera were detected as well, including Aliivibrio spp., Photobacterium spp., Pseudoalteromonas spp., Psychrilyobacter spp. and Mycoplasma spp. Bacteria of the genus Mycoplasma were in high abundance particularly in the sample originated from Limnos island representing the first time recorded in Pinna nobilis. In conclusion, apart from exclusively the Haplosporidan and the Mycobacterium parasites, the presence of potentially pathogenic bacterial taxa detected, such as Vibrio spp., Photobactrium spp. and Alivibrio spp. lead us to assume that mortality events in the endangered Fan mussel, Pinna nobilis, may be attributed to synergistic effects of more pathogens.},
}
@article {pmid33259824,
year = {2020},
author = {Wiemken, TL and Ericsson, AC},
title = {Chlorhexidine gluconate does not result in epidermal microbiota dysbiosis in healthy adults.},
journal = {American journal of infection control},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajic.2020.11.021},
pmid = {33259824},
issn = {1527-3296},
abstract = {BACKGROUND: Chlorhexidine gluconate (CHG) and other skin antiseptics are ubiquitous in healthcare settings and are routinely used to bathe patients' skin. The commensal epidermal microbiota is believed to provide colonization resistance and other benefits to the host; yet little is known regarding the long-term stability of the epidermal microbiota, and the impact of CHG bathing. We aimed to assess the influence of CHG exposure to the epidermal microbiota and evaluate the long-term stability of the epidermal microbiota.<br><br>METHODS: The epidermal microbiota of 5 individuals was sampled using thorough swabbing of the calf, and characterized via 16S rRNA amplicon sequencing, prior to CHG bathing, and then at 30 minutes, 3 hours, 1 day, 3 days, and 7 days postbathing. Roughly 4 months later, samples were collected from the same 5 individuals, using an identical timeline but with no CHG exposure.<br><br>RESULTS: The epidermal microbiota showed no greater change 30 minutes postexposure to CHG, than was observed in the same individuals during the recovery period, likely representing the normal sample-to-sample variability. Despite that variability, the epidermal microbiota evinced a remarkable degree of intrasubject stability, even over extended periods of time.<br><br>CONCLUSION: We conclude that single applications of CHG cause minimal, if any, disruption of the epidermal microbiota, and that long-term effects of single applications of CHG on the epidermal microbiota are unlikely.},
}
@article {pmid33259553,
year = {2020},
author = {, },
title = {Correction: Metagenomics analysis reveals features unique to Indian distal gut microbiota.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0243397},
pmid = {33259553},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0231197.].},
}
@article {pmid33259541,
year = {2020},
author = {Yu, G and Zhao, W and Shen, Y and Zhu, P and Zheng, H},
title = {Metagenomic next generation sequencing for the diagnosis of tuberculosis meningitis: A systematic review and meta-analysis.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0243161},
pmid = {33259541},
issn = {1932-6203},
abstract = {BACKGROUND: Tuberculous meningitis (TBM) is a severe form of extrapulmonary tuberculosis and its early diagnosis is very difficult leading to present with severe disability or die. The current study aimed to assess the accuracy of metagenomic next generation sequencing (mNGS) for TBM, and to identify a new test for the early diagnosis of TBM.<br><br>METHODS: We searched for articles published in Embase, PubMed, Cochrane Library, China National Knowledge Infrastructure, and Wanfang Data up to June 30, 2020 for studies that assessed the efficacy of mNGS for the diagnosis of TBM. Then, the accuracy between mNGS and a composite reference standard (CRS) in these articles was compared using the meta-analysis approach.<br><br>RESULTS: Four independent studies with 342 samples comparing mNGS and a CRS were included in this study. The sensitivity of mNGS for TBM diagnosis ranged from 27% to 84%. The combined sensitivity of mNGS was 61%, and the I2 value was 92%. Moreover, the specificity of mNGS for TBM diagnosis ranged from 96% to 100%. The combined specificity of mNGS was 98%, and the I2 value was 74%. The heterogeneity between studies in terms of sensitivity and specificity was significant. The area under the curve (AUC) of the summary receiver operating characteristic curve (SROC) of mNGS for TBM was 0.98.<br><br>CONCLUSIONS: The sensitivity of mNGS for TBM diagnosis was moderate. Furthermore, the specificity was extremely high, and the AUC of the SROC indicated a very good diagnostic efficacy. mNGS could be used as an early diagnostic method for TBM, however, the results should be treated with caution for the heterogeneity between studies was extremely significant.<br><br>INPLASY202070100.},
}
@article {pmid33258767,
year = {2020},
author = {Abbas, A and Taylor, LJ and Collman, RG and Bushman, FD and Ictv Report Consortium, },
title = {ICTV Virus Taxonomy Profile: Redondoviridae.},
journal = {The Journal of general virology},
volume = {},
number = {},
pages = {},
doi = {10.1099/jgv.0.001526},
pmid = {33258767},
issn = {1465-2099},
abstract = {Viruses in the family Redondoviridae have a circular genome of 3.0 kb with three open reading frames. The packaged genome is inferred to be single-stranded DNA by analogy to related viruses. Redondoviruses were discovered through metagenomic sequencing methods in samples from human subjects and are inferred to replicate in humans. Evidence of redondovirus infection is associated with periodontitis and critical illness, but redondoviruses have not been shown to be the causative agent of any diseases. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Redondoviridae, which is available at ictv.global/report/redondoviridae.},
}
@article {pmid33258724,
year = {2020},
author = {Dunn, KA and Connors, J and Bielawski, JP and Nearing, JT and Langille, MGI and Van Limbergen, J and Fernandez, CV and MacDonald, T and Kulkarni, K},
title = {Investigating the gut microbial community and genes in children with differing levels of change in serum asparaginase activity during pegaspargase treatment for acute lymphoblastic leukemia.},
journal = {Leukemia &amp; lymphoma},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/10428194.2020.1850718},
pmid = {33258724},
issn = {1029-2403},
abstract = {Asparaginase (ASNase) is an effective treatment of pediatric acute lymphoblastic leukemia (ALL). Changes in ASNase activity may lead to suboptimal treatment and poorer outcomes. The gut microbiome produces metabolites that could impact ASNase therapy, however, remains uninvestigated. We examined gut-microbial community and microbial-ASNase and asparagine synthetase (ASNS) genes using 16SrRNA and metagenomic sequence data from stool samples of pediatric ALL patients. Comparing ASNase activity between consecutive ASNase-doses, we found microbial communities differed between decreased- and increased-activity samples. Escherichia predominated in the decreased-activity community while Bacteroides and Streptococcus predominated in the increased-activity community. In addition microbial ASNS was significantly (p=.004) negatively correlated with change in serum ASNase activity. These preliminary findings suggest microbial communities prior to treatment could affect serum ASNase levels, although the mechanism is unknown. Replication in an independent cohort is needed, and future research on manipulation of these communities and genes could prove useful in optimizing ASNase therapy.},
}
@article {pmid33257863,
year = {2020},
author = {Kovaka, S and Fan, Y and Ni, B and Timp, W and Schatz, MC},
title = {Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41587-020-0731-9},
pmid = {33257863},
issn = {1546-1696},
support = {1R01HG009190//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; DBI-1350041//National Science Foundation (NSF)/ ; },
abstract = {Conventional targeted sequencing methods eliminate many of the benefits of nanopore sequencing, such as the ability to accurately detect structural variants or epigenetic modifications. The ReadUntil method allows nanopore devices to selectively eject reads from pores in real time, which could enable purely computational targeted sequencing. However, this requires rapid identification of on-target reads while most mapping methods require computationally intensive basecalling. We present UNCALLED (https://github.com/skovaka/UNCALLED), an open source mapper that rapidly matches streaming of nanopore current signals to a reference sequence. UNCALLED probabilistically considers k-mers that could be represented by the signal and then prunes the candidates based on the reference encoded within a Ferragina-Manzini index. We used UNCALLED to deplete sequencing of known bacterial genomes within a metagenomics community, enriching the remaining species 4.46-fold. UNCALLED also enriched 148 human genes associated with hereditary cancers to 29.6× coverage using one MinION flowcell, enabling accurate detection of single-nucleotide polymorphisms, insertions and deletions, structural variants and methylation in these genes.},
}
@article {pmid33257813,
year = {2020},
author = {Fones, EM and Colman, DR and Kraus, EA and Stepanauskas, R and Templeton, AS and Spear, JR and Boyd, ES},
title = {Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-020-00838-1},
pmid = {33257813},
issn = {1751-7370},
support = {NNA15BB02A//NASA | NASA Astrobiology Institute (NAI)/ ; NNA15BB02A//NASA | NASA Astrobiology Institute (NAI)/ ; },
abstract = {Metagenome assembled genomes (MAGs) and single amplified genomes (SAGs) affiliated with two distinct Methanobacterium lineages were recovered from subsurface fracture waters of the Samail Ophiolite, Sultanate of Oman. Lineage Type I was abundant in waters with circumneutral pH, whereas lineage Type II was abundant in hydrogen rich, hyperalkaline waters. Type I encoded proteins to couple hydrogen oxidation to CO2 reduction, typical of hydrogenotrophic methanogens. Surprisingly, Type II, which branched from the Type I lineage, lacked homologs of two key oxidative [NiFe]-hydrogenases. These functions were presumably replaced by formate dehydrogenases that oxidize formate to yield reductant and cytoplasmic CO2 via a pathway that was unique among characterized Methanobacteria, allowing cells to overcome CO2/oxidant limitation in high pH waters. This prediction was supported by microcosm-based radiotracer experiments that showed significant biological methane generation from formate, but not bicarbonate, in waters where the Type II lineage was detected in highest relative abundance. Phylogenetic analyses and variability in gene content suggested that recent and ongoing diversification of the Type II lineage was enabled by gene transfer, loss, and transposition. These data indicate that selection imposed by CO2/oxidant availability drove recent methanogen diversification into hyperalkaline waters that are heavily impacted by serpentinization.},
}
@article {pmid33256173,
year = {2020},
author = {Truchado, DA and Llanos-Garrido, A and Oropesa-Olmedo, DA and Cerrada, B and Cea, P and Moens, MAJ and Gomez-Lucia, E and Doménech, A and Milá, B and Pérez-Tris, J and Cadar, D and Benítez, L},
title = {Comparative Metagenomics of Palearctic and Neotropical Avian Cloacal Viromes Reveal Geographic Bias in Virus Discovery.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33256173},
issn = {2076-2607},
support = {CGL2013-41642-P/BOS//Spanish National Research Agency/ ; CGL2017-82117-P//Spanish National Research Agency/ ; CEBA2015-TROCSYMB//ANR/ ; CEBA:ANR-10-LABX-25-01//ANR/ ; CT27/16-CT28/16//Complutense University of Madrid/ ; },
abstract = {Our understanding about viruses carried by wild animals is still scarce. The viral diversity of wildlife may be best described with discovery-driven approaches to the study of viral diversity that broaden research efforts towards non-canonical hosts and remote geographic regions. Birds have been key organisms in the transmission of viruses causing important diseases, and wild birds are threatened by viral spillovers associated with human activities. However, our knowledge of the avian virome may be biased towards poultry and highly pathogenic diseases. We describe and compare the fecal virome of two passerine-dominated bird assemblages sampled in a remote Neotropical rainforest in French Guiana (Nouragues Natural Reserve) and a Mediterranean forest in central Spain (La Herrería). We used metagenomic data to quantify the degree of functional and genetic novelty of viruses recovered by examining if the similarity of the contigs we obtained to reference sequences differed between both locations. In general, contigs from Nouragues were significantly less similar to viruses in databases than contigs from La Herrería using Blastn but not for Blastx, suggesting that pristine regions harbor a yet unknown viral diversity with genetically more singular viruses than more studied areas. Additionally, we describe putative novel viruses of the families Picornaviridae, Reoviridae and Hepeviridae. These results highlight the importance of wild animals and remote regions as sources of novel viruses that substantially broaden the current knowledge of the global diversity of viruses.},
}
@article {pmid33255785,
year = {2020},
author = {Hazan, S and Spradling-Reeves, KD and Papoutsis, A and Walker, SJ},
title = {Shotgun Metagenomic Sequencing Identifies Dysbiosis in Triplet Sibling with Gastrointestinal Symptoms and ASD.},
journal = {Children (Basel, Switzerland)},
volume = {7},
number = {12},
pages = {},
pmid = {33255785},
issn = {2227-9067},
abstract = {The gut microbiome profile of a child with autism spectrum disorder (ASD) and co-occurring gastrointestinal (GI) symptoms was compared to that of her healthy triplet siblings to determine if she exhibited intestinal dysbiosis. Shotgun metagenomic sequencing was performed in individual fecal samples, and relative microbial abundance and diversity was determined. Microbial diversity was lower in sibling #3, coupled with a higher Bacteroidetes/Firmicutes ratio, a lower relative abundance of Actinobacteria, and an increased relative abundance of Proteobacteria. Our findings are suggestive of gut dysbiosis in a child with ASD and co-occurring GI symptoms, compared to her two healthy triplet siblings.},
}
@article {pmid33255715,
year = {2020},
author = {Sala, C and Mordhorst, H and Grützke, J and Brinkmann, A and Petersen, TN and Poulsen, C and Cotter, PD and Crispie, F and Ellis, RJ and Castellani, G and Amid, C and Hakhverdyan, M and Guyader, SL and Manfreda, G and Mossong, J and Nitsche, A and Ragimbeau, C and Schaeffer, J and Schlundt, J and Tay, MYF and Aarestrup, FM and Hendriksen, RS and Pamp, SJ and De Cesare, A},
title = {Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33255715},
issn = {2076-2607},
support = {643476//European Commission/ ; },
abstract = {An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members spiked in the cold smoked salmon, were both detected and quantified in terms of relative abundance, in the metagenomic datasets, proving the suitability of shotgun metagenomic sequencing as a genomic tool to detect microorganisms belonging to different domains in the same food matrix. The implementation of standardized wet-lab protocols would highly facilitate the comparability of shotgun metagenomic sequencing dataset across laboratories and sectors. Moreover, there is a need for clearly defining a sequencing reads threshold, to consider pathogens as detected or undetected in a food sample.},
}
@article {pmid33255677,
year = {2020},
author = {Ticinesi, A and Mancabelli, L and Tagliaferri, S and Nouvenne, A and Milani, C and Del Rio, D and Lauretani, F and Maggio, MG and Ventura, M and Meschi, T},
title = {The Gut-Muscle Axis in Older Subjects with Low Muscle Mass and Performance: A Proof of Concept Study Exploring Fecal Microbiota Composition and Function with Shotgun Metagenomics Sequencing.},
journal = {International journal of molecular sciences},
volume = {21},
number = {23},
pages = {},
pmid = {33255677},
issn = {1422-0067},
support = {FIL Quota Incentivante 2016-17//University of Parma/ ; },
abstract = {The gut microbiota could influence the pathophysiology of age-related sarcopenia through multiple mechanisms implying modulation of chronic inflammation and anabolic resistance. The aim of this study was to compare the fecal microbiota composition and functionality, assessed by shotgun metagenomics sequencing, between two groups of elderly outpatients, differing only for the presence of primary sarcopenia. Five sarcopenic elderly subjects and twelve non-sarcopenic controls, classified according to lower limb function and bioimpedance-derived skeletal muscle index, provided a stool sample, which was analyzed with shotgun metagenomics approaches, to determine the overall microbiota composition, the representation of bacteria at the species level, and the prediction of bacterial genes involved in functional metabolic pathways. Sarcopenic subjects displayed different fecal microbiota compositions at the species level, with significant depletion of two species known for their metabolic capacity of producing short-chain fatty acids (SCFAs), Faecalibacterium prausnitzii and Roseburia inulinivorans, and of Alistipes shahii. Additionally, their fecal metagenome had different representation of genes belonging to 108 metabolic pathways, namely, depletion of genes involved in SCFA synthesis, carotenoid and isoflavone biotransformation, and amino acid interconversion. These results support the hypothesis of an association between microbiota and sarcopenia, indicating novel possible mediators, whose clinical relevance should be investigated in future studies.},
}
@article {pmid33255324,
year = {2020},
author = {Pramanik, K and Das, A and Banerjee, J and Das, A and Chatterjee, S and Sharma, R and Kumar, S and Gupta, S},
title = {Metagenomic Insights into Rhizospheric Microbiome Profiling in Lentil Cultivars Unveils Differential Microbial Nitrogen and Phosphorus Metabolism under Rice-Fallow Ecology.},
journal = {International journal of molecular sciences},
volume = {21},
number = {23},
pages = {},
pmid = {33255324},
issn = {1422-0067},
abstract = {The plant rhizosphere interfaces an array of microbiomes related to plant growth and development. Cultivar-specific soil microbial communities with respect to their taxonomic structure and specific function have not been investigated explicitly in improving the adaptation of lentil cultivars under rice-fallow ecology. The present study was carried out to decipher the rhizosphere microbiome assembly of two lentil cultivars under rice-fallow ecology for discerning the diversity of microbial communities and for predicting the function of microbiome genes related to nitrogen (N) and phosphorus (P) cycling processes deploying high-throughput whole (meta) genome sequencing. The metagenome profile of two cultivars detected variable microbiome composition with discrete metabolic activity. Cyanobacteria, Bacteroidetes, Proteobacteria, Gemmatimonadetes, and Thaumarchaeota were abundant phyla in the &quot;Farmer-2&quot; rhizosphere, whereas Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Chloroflexi, and some incompletely described procaryotes of the &quot;Candidatus&quot; category were found to be robustly enriched the rhizosphere of &quot;Moitree&quot;. Functional prediction profiles of the microbial metagenomes between two cultivars revealed mostly house keeping genes with general metabolism. Additionally, the rhizosphere of &quot;Moitree&quot; had a high abundance of genes related to denitrification processes. Significant difference was observed regarding P cycling genes between the cultivars. &quot;Moitree&quot; with a profuse root system exhibited better N fixation and translocation ability due to a good &quot;foraging strategy&quot; for improving acquisition of native P under the nutrient depleted rice-fallow ecology. However, &quot;Farmer-2&quot; revealed a better &quot;mining strategy&quot; for enhancing P solubilization and further transportation to sinks. This study warrants comprehensive research for explaining the role of microbiome diversity and cultivar-microbe interactions towards stimulating microbiome-derived soil reactions regarding nutrient availability under rice-fallow ecology.},
}
@article {pmid33254887,
year = {2021},
author = {Yang, Q and Rivailler, P and Zhu, S and Yan, D and Xie, N and Tang, H and Zhang, Y and Xu, W},
title = {Detection of multiple viruses potentially infecting humans in sewage water from Xinjiang Uygur Autonomous Region, China.},
journal = {The Science of the total environment},
volume = {754},
number = {},
pages = {142322},
doi = {10.1016/j.scitotenv.2020.142322},
pmid = {33254887},
issn = {1879-1026},
mesh = {China ; Humans ; Metagenomics ; *Papillomaviridae ; *Sewage ; Water ; },
abstract = {The progress of sequencing technologies has facilitated metagenomics projects on environmental samples like sewage water. The present study concerned the analysis of sewage samples collected from 3 locations in Xinjiang Uygur Autonomous Region in China. The analysis focused on RNA viruses known to infect humans and identified viruses from 10 families. The proportion of human virus species in the sewage samples was relatively stable with an average of 17%. Thirty virus species known to infect humans were identified and they belonged to 6 families: Picornaviridae (12), Astroviridae (11), Reoviridae (3), Caliciviridae (2), Papillomaviridae (1) and Picobirnaviridae (1). A total of 16 full-length genomes were generated from Astroviridae, Picornaviridae (Salivirus and Kobuvirus) and Picobirnaviridae. Astroviruses appeared to be the most present viruses and were detected in all sewage samples. Analyzing the virome of sewage samples should help to monitor any potential risks to public health.},
}
@article {pmid33254605,
year = {2020},
author = {Aguiar, LM and Souza, MF and de Laia, ML and de Oliveira Melo, J and da Costa, MR and Gonçalves, JF and Silva, DV and Dos Santos, JB},
title = {Metagenomic analysis reveals mechanisms of atrazine biodegradation promoted by tree species.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {267},
number = {},
pages = {115636},
doi = {10.1016/j.envpol.2020.115636},
pmid = {33254605},
issn = {1873-6424},
mesh = {*Atrazine ; Biodegradation, Environmental ; *Herbicides ; Metagenome ; Soil Microbiology ; *Soil Pollutants/analysis ; Trees ; },
abstract = {Metagenomics has provided the discovery of genes and metabolic pathways involved in the degradation of xenobiotics. Some microorganisms can metabolize these compounds, potentiating phytoremediation in association with plant. This study aimed to study the metagenome and the occurrence of atrazine degradation genes in rhizospheric soils of the phytoremediation species Inga striata and Caesalphinea ferrea. The genera of microorganisms predominant in the rhizospheric soils of I. striata and C. ferrea were Mycobacterium, Conexibacter, Bradyrhizobium, Solirubrobacter, Rhodoplanes, Streptomyces, Geothrix, Gaiella, Nitrospira, and Haliangium. The atzD, atzE, and atzF genes were detected in the rhizospheric soils of I. striata and atzE and atzF in the rhizospheric soils of C. ferrea. The rhizodegradation by both tree species accelerates the degradation of atrazine residues, eliminating toxic effects on plants highly sensitive to this herbicide. This is the first report for the species Agrobacterium rhizogenes and Candidatus Muproteobacteria bacterium and Micromonospora genera as atrazine degraders.},
}
@article {pmid33254468,
year = {2021},
author = {Okurowska, K and Karunakaran, E and Al-Farttoosy, A and Couto, N and Pandhal, J},
title = {Adapting the algal microbiome for growth on domestic landfill leachate.},
journal = {Bioresource technology},
volume = {319},
number = {},
pages = {124246},
doi = {10.1016/j.biortech.2020.124246},
pmid = {33254468},
issn = {1873-2976},
mesh = {Biodegradation, Environmental ; *Chlorella vulgaris ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/analysis ; },
abstract = {We aimed to improve algal growth rate on leachate by optimising the algal microbiome. An algal-bacterial consortium was enriched from landfill leachate and subjected to 24 months of adaptive laboratory evolution, increasing the growth rate of the dominant algal strain, Chlorella vulgaris, almost three-fold to 0.2 d-1. A dramatic reduction in nitrate production suggested a shift in biological utilisation of ammoniacal-N, supported by molecular 16S rRNA taxonomic analyses, where Nitrosomonas numbers were not detected in the adapted consortium. A PICRUSt approach predicted metagenomic functional content and revealed a high number of sequences belonging to bioremediation pathways, including degradation of aromatic compounds, benzoate and naphthalene, as well as pathways known to be involved in algal-bacterial symbiosis. This study enhances our understanding of beneficial mechanisms in algal-bacterial associations in complex effluents, and ultimately enables the bottom-up design of optimised algal microbiomes for exploitation within industry.},
}
@article {pmid33253304,
year = {2020},
author = {Yu, K and Zhang, T},
title = {Correction: Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge.},
journal = {PloS one},
volume = {15},
number = {11},
pages = {e0243233},
pmid = {33253304},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0038183.].},
}
@article {pmid33253207,
year = {2020},
author = {Yahara, H and Hiraki, A and Maruoka, Y and Hirabayashi, A and Suzuki, M and Yahara, K},
title = {Shotgun metagenome sequencing identification of a set of genes encoded by Actinomyces associated with medication-related osteonecrosis of the jaw.},
journal = {PloS one},
volume = {15},
number = {11},
pages = {e0241676},
pmid = {33253207},
issn = {1932-6203},
abstract = {Medication-related osteonecrosis of the jaw (MRONJ) is intractable and severely affects a patient's quality of life. Although many cases of MRONJ have been reported in the past decade, the disease pathophysiology is unclear and there are no evidence-based therapeutic strategies. MRONJ usually features bone inflammation and infection. Prior studies that explored the association between MRONJ and microbial infection used the culture-based approach, which is not applicable to hundreds of unculturable taxa in the human oral microbiome, or 16S ribosomal RNA gene sequencing, which does not provide quantitative information of the abundance of specific taxa, and information of the presence, abundance, and function of specific genes in the microbiome. Here, deep shotgun metagenome sequencing (>10 Gb per sample) of bulk DNA extracted from saliva of MRONJ patients and healthy controls was performed to overcome these limitations. Comparative quantitative analyses of taxonomic and functional composition of these deep metagenomes (initially of 5 patients and 5 healthy controls) revealed an average 10.1% increase of genus Actinomyces and a 33.2% decrease in genus Streptococcus normally predominant in the human oral microbiota. Pan-genome analysis identified genes present exclusively in the MRONJ samples. Further analysis of the reads mapping to the genes in the extended dataset comprising five additional MRONJ samples and publicly available dataset of nine healthy controls resulted in the identification of 31 genes significantly associated with MRONJ. All these genes were encoded by Actinomyces genomic regions. Of these, the top two abundant genes were almost exclusively encoded by Actinomyces among usual taxa in the human oral microbiota. The potential relationships of these key genes with the disease are discussed at molecular level based on the literature. Although the sample size was small, this study will aid future studies to verify the data and characterize these genes in vitro and in vivo to understand the disease mechanisms, develop molecular targeted drugs, and for early stage screening and prognosis prediction.},
}
@article {pmid33253058,
year = {2020},
author = {Soliman, MS and AbdelFattah, M and Aman, SMN and Ibrahim, LM and Aziz, RK},
title = {A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/omi.2020.0194},
pmid = {33253058},
issn = {1557-8100},
abstract = {The novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is causing an unprecedented pandemic, threatening planetary health, society, and economy. Genomic surveillance continues to be a critical effort toward tracking the virus and containing its spread, and more genomes from diverse geographical areas and different time points are needed to provide an appropriate representation of the virus evolution. In this study, we report the successful assembly of one single gapless, unambiguous contiguous sequence representing the complete viral genome from a nasopharyngeal swab of an infected health care worker in Cairo, Egypt. The sequence has all typical features of SARS-CoV-2 genomes, with no protein-disrupting mutations. However, three mutations are worth highlighting and future tracking: a synonymous mutation causing a rare spike S813I variation and two less frequent ones leading to an A41V variation in NSP3, encoded by ORF1a (ORF1a A895V), and a Q677H variation in the spike protein. Both affected proteins, S and NSP3, are relevant to vaccine and drug development. Although the genome, named CU_S3, belongs to the prevalent global genotype, marked by the D614G spike variation, the combined variations in the spike proteins and ORF1a do not co-occur in any of the 197,000 genomes reported to date. Future studies will assess the biological, pathogenic, and epidemiological implications of this set of genetic variations. This line of research is needed to inform vaccine and therapeutic innovation to stem the COVID-19 pandemic.},
}
@article {pmid33252655,
year = {2020},
author = {Weißbecker, C and Schnabel, B and Heintz-Buschart, A},
title = {Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.},
journal = {GigaScience},
volume = {9},
number = {12},
pages = {},
pmid = {33252655},
issn = {2047-217X},
abstract = {BACKGROUND: Amplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities. Microbial ecologists often have expert knowledge on their biological question and data analysis in general, and most research institutes have computational infrastructures to use the bioinformatics command line tools and workflows for amplicon sequencing analysis, but requirements of bioinformatics skills often limit the efficient and up-to-date use of computational resources.<br><br>RESULTS: We present dadasnake, a user-friendly, 1-command Snakemake pipeline that wraps the preprocessing of sequencing reads and the delineation of exact sequence variants by using the favorably benchmarked and widely used DADA2 algorithm with a taxonomic classification and the post-processing of the resultant tables, including hand-off in standard formats. The suitability of the provided default configurations is demonstrated using mock community data from bacteria and archaea, as well as fungi.<br><br>CONCLUSIONS: By use of Snakemake, dadasnake makes efficient use of high-performance computing infrastructures. Easy user configuration guarantees flexibility of all steps, including the processing of data from multiple sequencing platforms. It is easy to install dadasnake via conda environments. dadasnake is available at https://github.com/a-h-b/dadasnake.},
}
@article {pmid33251246,
year = {2020},
author = {Quan, W and Guan, D and Quan, G and Liu, B and Wang, Y},
title = {Short Read Alignment Based on Maximal Approximate Match Seeds.},
journal = {Frontiers in molecular biosciences},
volume = {7},
number = {},
pages = {572934},
pmid = {33251246},
issn = {2296-889X},
abstract = {Sequence alignment is a critical step in many critical genomic studies, such as variant calling, quantitative transcriptome analysis (RNA-seq), and metagenomic sequence classification. However, the alignment performance is largely affected by repetitive sequences in the reference genome, which extensively exist in species from bacteria to mammals. Aligning repeating sequences might lead to tremendous candidate locations, bringing about a challenging computational burden. Thus, most alignment tools prefer to simply discard highly repetitive seeds, but this may cause the true alignment to be missed. Using maximal approximate matches (MAMs) as seeds is an option, but MEMs seeds may fail due to sequencing errors or genomic variations in MEMs seeds. Here, we propose a novel sequence alignment algorithm, named MAM, which can efficiently align short DNA sequences. MAM first builds a modified Burrows-Wheeler transform (BWT) structure of a reference genome to accelerate approximate seed matching. Then, MAM uses maximal approximate matches (MAMs) seeds to reduce th